I very interested in this. Currently XFS in kernel v 4.14 is the most promising.
Just a short summary from my previous investigation: if SELinux is not an issue then one can implement deduplication with FUSE or hack it with OverlayFS. The latter is more Copy-on-Write though.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromiumos/overlays/portage-stable/+/91e8bc7a1454b4b007db2e03cca828368ad5259a

commit 91e8bc7a1454b4b007db2e03cca828368ad5259a
Author: Gwendal Grignou <gwendal@chromium.org>
Date: Wed May 30 19:50:37 2018

xfsprogs: upgraded package to upstream

Upgraded sys-fs/xfsprogs to version 4.14.0 on amd64, arm, x86

Command used:
cros_portage_upgrade --board=eve-arcnext:kevin:x86-generic --upgrade
sys-fs/xfsprogs

BUG= chromium:846756 
TEST=deploy on eve-arcnext, run xfstest.

Change-Id: I24f62fabdde4ee3a0cd06755193ec49391d95ec4
Signed-off-by: Gwendal Grignou <gwendal@chromium.org>
Reviewed-on: https://chromium-review.googlesource.com/1072458
Reviewed-by: Mike Frysinger <vapier@chromium.org>

[add] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/sys-fs/xfsprogs/files/xfsprogs-4.7.0-libxcmd-link.patch
[rename] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/sys-fs/xfsprogs/xfsprogs-4.14.0.ebuild
[rename] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/sys-fs/xfsprogs/files/xfsprogs-4.12.0-sharedlibs.patch
[modify] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/sys-fs/xfsprogs/Manifest
[rename] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/metadata/md5-cache/sys-fs/xfsprogs-4.14.0
[delete] https://crrev.com/a3ba3fa4d8e03d08a89fcdcd272cec51f6e1900e/sys-fs/xfsprogs/files/xfsprogs-4.3.0-cross-compile.patch
[delete] https://crrev.com/a3ba3fa4d8e03d08a89fcdcd272cec51f6e1900e/sys-fs/xfsprogs/files/xfsprogs-4.5.0-linguas.patch
[modify] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/sys-fs/xfsprogs/metadata.xml
[add] https://crrev.com/91e8bc7a1454b4b007db2e03cca828368ad5259a/sys-fs/xfsprogs/files/xfsprogs-4.9.0-underlinking.patch

Current plan is to deduplicate in user space, be apk specific.