https://chromium.googlesource.com/chromium/src/+/master/tools/gn/docs/reference.md#What-gets-checked


> gn check
> [...]
> What gets checked
> [...]
>    - Include paths are assumed to be relative to either the source root or the
>      "root_gen_dir" and must include all the path components. (It might be
>      nice in the future to incorporate GN's knowledge of the include path to
>      handle other include styles.)

The generated header actually ends up at blink/platform/RuntimeEnabledFeatures.h

If I update the #include to use the full path instead, then gn check is able to detect the missing dependency:

ERROR at //third_party/WebKit/Source/platform/scheduler/renderer/web_view_scheduler_impl.cc:11:11: Include not allowed.
#include "blink/platform/RuntimeEnabledFeatures.h"
          ^--------------------------------------
It is not in any dependency of
  //third_party/WebKit/Source/platform/scheduler:scheduler
The include file is in the target(s):
  //third_party/WebKit/Source/platform:platform
  //third_party/WebKit/Source/platform:runtime_enabled_features
at least one of which should somehow be reachable.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/05e6a0b4f200f584ee0a7d1e8e4302933fa04c1f

commit 05e6a0b4f200f584ee0a7d1e8e4302933fa04c1f
Author: Mike Bjorge <mbjorge@chromium.org>
Date: Tue Aug 08 11:07:57 2017

Add dep for scheduler/render to RuntimeEnabledFeatures.h

Several scheduler/renderer/* files reference RuntimeEnabledFeatures.h.
This file is generated from a template though, so there needs to be a
GN dep on to the make_platform_generated target to make sure the file
will always exists in time.

Bug:  753171 
Change-Id: Id383a467b473ccd80508af76d1a02d9a29fbfa60
Reviewed-on: https://chromium-review.googlesource.com/604401
Reviewed-by: Alex Clarke <alexclarke@chromium.org>
Reviewed-by: Alexander Timin <altimin@chromium.org>
Commit-Queue: Alexander Timin <altimin@chromium.org>
Cr-Commit-Position: refs/heads/master@{#492591}
[modify] https://crrev.com/05e6a0b4f200f584ee0a7d1e8e4302933fa04c1f/third_party/WebKit/Source/platform/scheduler/BUILD.gn