One more data point:

[31177/39825] CXX newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/pipe_control_messages.mojom.o
FAILED: newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/pipe_control_messages.mojom.o 
/b/c/goma_client/gomacc ../../native_client/toolchain/linux_x86/pnacl_newlib/bin/pnacl-clang++ -MMD -MF newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/pipe_control_messages.mojom.o.d -DNACL_TC_REV=b48266b051f596802addff7c8d1fc6fb9cf6bea7 -DIS_MOJO_MOJOM_BINDINGS_IMPL -DV8_DEPRECATION_WARNINGS -DNO_TCMALLOC -DFULL_SAFE_BROWSING -DSAFE_BROWSING_CSD -DSAFE_BROWSING_DB_LOCAL -DOFFICIAL_BUILD -DGOOGLE_CHROME_BUILD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DCR_CLANG_REVISION=\"325667-1\" -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -DNDEBUG -DNVALGRIND -I../../native_client/src/public/linux_syscalls -I../.. -Inewlib_pnacl_nonsfi/gen -fno-strict-aliasing -fcolor-diagnostics --pnacl-allow-translate -arch x86-32-nonsfi --pnacl-bias=x86-32-nonsfi --target=i686-unknown-nacl -Wall -Werror -Wextra -Wimplicit-fallthrough -Wthread-safety -Wno-missing-field-initializers -Wno-unused-parameter -Wno-c++11-narrowing -Wno-covered-switch-default -Wno-unneeded-internal-declaration -Wno-inconsistent-missing-override -O2 -fno-ident -fdata-sections -ffunction-sections -fomit-frame-pointer -g2 -fvisibility=hidden -std=gnu++14 -fno-exceptions -fno-rtti -fvisibility-inlines-hidden -c newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/pipe_control_messages.mojom.cc -o newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/pipe_control_messages.mojom.o
In file included from newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/pipe_control_messages.mojom.cc:15:
newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/pipe_control_messages.mojom.h:18:10: fatal error: 'mojo/public/cpp/bindings/mojo_features.h' file not found
#include "mojo/public/cpp/bindings/mojo_features.h"
         ^
1 error generated.
[31178/39825] CXX newlib_pnacl_nonsfi/obj/base/base/values.o
[31179/39825] CXX newlib_pnacl_nonsfi/obj/base/base/memory_peak_detector.o
[31180/39825] ACTION //content/public/common:service_names__type_mappings(//build/toolchain/nacl:newlib_pnacl_nonsfi)
[31181/39825] CXX newlib_pnacl_nonsfi/obj/base/base/memory_allocator_dump.o
[31182/39825] CXX newlib_pnacl_nonsfi/obj/gpu/command_buffer/client/gles2_implementation/client_context_state.o
[31183/39825] CXX newlib_pnacl_nonsfi/obj/gpu/command_buffer/client/gles2_implementation/buffer_tracker.o
[31184/39825] CXX newlib_pnacl_nonsfi/obj/base/base/trace_buffer.o
[31185/39825] CXX newlib_pnacl_nonsfi/obj/base/base/memory_usage_estimator.o
[31186/39825] CXX newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/interface_control_messages.mojom.o
FAILED: newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/interface_control_messages.mojom.o 
/b/c/goma_client/gomacc ../../native_client/toolchain/linux_x86/pnacl_newlib/bin/pnacl-clang++ -MMD -MF newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/interface_control_messages.mojom.o.d -DNACL_TC_REV=b48266b051f596802addff7c8d1fc6fb9cf6bea7 -DIS_MOJO_MOJOM_BINDINGS_IMPL -DV8_DEPRECATION_WARNINGS -DNO_TCMALLOC -DFULL_SAFE_BROWSING -DSAFE_BROWSING_CSD -DSAFE_BROWSING_DB_LOCAL -DOFFICIAL_BUILD -DGOOGLE_CHROME_BUILD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DCR_CLANG_REVISION=\"325667-1\" -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -DNDEBUG -DNVALGRIND -I../../native_client/src/public/linux_syscalls -I../.. -Inewlib_pnacl_nonsfi/gen -fno-strict-aliasing -fcolor-diagnostics --pnacl-allow-translate -arch x86-32-nonsfi --pnacl-bias=x86-32-nonsfi --target=i686-unknown-nacl -Wall -Werror -Wextra -Wimplicit-fallthrough -Wthread-safety -Wno-missing-field-initializers -Wno-unused-parameter -Wno-c++11-narrowing -Wno-covered-switch-default -Wno-unneeded-internal-declaration -Wno-inconsistent-missing-override -O2 -fno-ident -fdata-sections -ffunction-sections -fomit-frame-pointer -g2 -fvisibility=hidden -std=gnu++14 -fno-exceptions -fno-rtti -fvisibility-inlines-hidden -c newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/interface_control_messages.mojom.cc -o newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/interface_control_messages.mojom.o
In file included from newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/interface_control_messages.mojom.cc:15:
newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/interface_control_messages.mojom.h:18:10: fatal error: 'mojo/public/cpp/bindings/mojo_features.h' file not found
#include "mojo/public/cpp/bindings/mojo_features.h"
         ^
1 error generated.
[31187/39825] AR newlib_pnacl_nonsfi/obj/components/nacl/common/libswitches.a
[31188/39825] CXX newlib_pnacl_nonsfi/obj/base/base/memory_dump_manager.o
[31189/39825] CXX newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/native_struct.mojom.o
FAILED: newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/native_struct.mojom.o 
/b/c/goma_client/gomacc ../../native_client/toolchain/linux_x86/pnacl_newlib/bin/pnacl-clang++ -MMD -MF newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/native_struct.mojom.o.d -DNACL_TC_REV=b48266b051f596802addff7c8d1fc6fb9cf6bea7 -DIS_MOJO_MOJOM_BINDINGS_IMPL -DV8_DEPRECATION_WARNINGS -DNO_TCMALLOC -DFULL_SAFE_BROWSING -DSAFE_BROWSING_CSD -DSAFE_BROWSING_DB_LOCAL -DOFFICIAL_BUILD -DGOOGLE_CHROME_BUILD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DCR_CLANG_REVISION=\"325667-1\" -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -DNDEBUG -DNVALGRIND -I../../native_client/src/public/linux_syscalls -I../.. -Inewlib_pnacl_nonsfi/gen -fno-strict-aliasing -fcolor-diagnostics --pnacl-allow-translate -arch x86-32-nonsfi --pnacl-bias=x86-32-nonsfi --target=i686-unknown-nacl -Wall -Werror -Wextra -Wimplicit-fallthrough -Wthread-safety -Wno-missing-field-initializers -Wno-unused-parameter -Wno-c++11-narrowing -Wno-covered-switch-default -Wno-unneeded-internal-declaration -Wno-inconsistent-missing-override -O2 -fno-ident -fdata-sections -ffunction-sections -fomit-frame-pointer -g2 -fvisibility=hidden -std=gnu++14 -fno-exceptions -fno-rtti -fvisibility-inlines-hidden -c newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/native_struct.mojom.cc -o newlib_pnacl_nonsfi/obj/mojo/public/interfaces/bindings/bindings/native_struct.mojom.o
In file included from newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/native_struct.mojom.cc:15:
newlib_pnacl_nonsfi/gen/mojo/public/interfaces/bindings/native_struct.mojom.h:18:10: fatal error: 'mojo/public/cpp/bindings/mojo_features.h' file not found
#include "mojo/public/cpp/bindings/mojo_features.h"
         ^
1 error generated.

https://logs.chromium.org/v/?s=chromium%2Fbb%2Fchromium.chrome%2FGoogle_Chrome_Linux_x64%2F28532%2F%2B%2Frecipes%2Fsteps%2Fcompile%2F0%2Fstdout

This is probably becuase the mojom_component rule in //src/mojo/public/interface/bindings/BUILD.gn sets disallow_native_types and disallow_interfaces, which causes the mojom rule to set require_full_cpp_deps to false which results in a dependency on on //mojo/public/cpp/bindings:bindings_base rather than :bindings. And only :bindings depends on the target that defines mojo_features.h. Should probably move that dependency to bindings_base?

given the timing, https://chromium.googlesource.com/chromium/src/+/015487b3149a59a17fd55e90cc82af1f9b551bbe looks somewhat suspicious as a proximate cause

It might have made it worse/more likely to trigger the flakiness, but I'm pretty sure of my analysis which would point to https://chromium-review.googlesource.com/c/chromium/src/+/893655 as the actual cause (where the broken dependency was introduced).

Yeah, didn't mean to suggest that your analysis was wrong; just looking for why the apparent frequency of the issue has jumped.

+rockot re mek's suggestion in #2, which sounds reasonable to me

... actually, given the tree closure, I'm just going to land that suggestion as https://chromium-review.googlesource.com/c/chromium/src/+/957462

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/c5db46b67fdd7509e003dcb17f6021f2251073be

commit c5db46b67fdd7509e003dcb17f6021f2251073be
Author: John Budorick <jbudorick@chromium.org>
Date: Fri Mar 09 20:56:13 2018

mojo: make bindings_base rather than bindings depend on mojo_features.

TBR=rockot@chromium.org

No-Tree-Checks: true
No-Try: true
Bug:  820407 
Change-Id: Ib10cd0c33aa8ad1725c22e180aa679352cd8883d
Reviewed-on: https://chromium-review.googlesource.com/957462
Commit-Queue: John Budorick <jbudorick@chromium.org>
Reviewed-by: Hongchan Choi <hongchan@chromium.org>
Cr-Commit-Position: refs/heads/master@{#542214}
[modify] https://crrev.com/c5db46b67fdd7509e003dcb17f6021f2251073be/mojo/public/cpp/bindings/BUILD.gn