finnur@, by any chance, could you point to me where the check is made so I could do this change when the flag has landed? You can also own this and I can ping you with the flag name when it's ready. As you prefer :)

You referring to this?

https://cs.chromium.org/chromium/src/chrome/android/java/src/org/chromium/chrome/browser/preferences/website/SiteSettingsPreferences.java?sq=package:chromium&l=71

Yes. Thanks! :)

Started looking into this.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/5d05e65d8ab098888e1e87cd51f93496e93a8398

commit 5d05e65d8ab098888e1e87cd51f93496e93a8398
Author: avayvod <avayvod@chromium.org>
Date: Fri Jun 10 16:04:46 2016

[Android, Media] Enable autoplay settings for muted autoplay, wired them up to the media element.

Use chrome://flags/#enable-autoplay-muted-videos to enable the autoplay site setting.

Check the setting before allowing muted videos to autoplay.

BUG= 618083 , 618081 
TEST=Manual

Review-Url: https://codereview.chromium.org/2052623002
Cr-Commit-Position: refs/heads/master@{#399199}

[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/chrome/android/java/src/org/chromium/chrome/browser/preferences/website/SiteSettingsPreferences.java
[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/third_party/WebKit/LayoutTests/media/autoplay-muted.html
[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/third_party/WebKit/Source/core/html/HTMLMediaElement.cpp
[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/third_party/WebKit/Source/core/html/HTMLMediaElement.h

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/5d05e65d8ab098888e1e87cd51f93496e93a8398

commit 5d05e65d8ab098888e1e87cd51f93496e93a8398
Author: avayvod <avayvod@chromium.org>
Date: Fri Jun 10 16:04:46 2016

[Android, Media] Enable autoplay settings for muted autoplay, wired them up to the media element.

Use chrome://flags/#enable-autoplay-muted-videos to enable the autoplay site setting.

Check the setting before allowing muted videos to autoplay.

BUG= 618083 , 618081 
TEST=Manual

Review-Url: https://codereview.chromium.org/2052623002
Cr-Commit-Position: refs/heads/master@{#399199}

[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/chrome/android/java/src/org/chromium/chrome/browser/preferences/website/SiteSettingsPreferences.java
[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/third_party/WebKit/LayoutTests/media/autoplay-muted.html
[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/third_party/WebKit/Source/core/html/HTMLMediaElement.cpp
[modify] https://crrev.com/5d05e65d8ab098888e1e87cd51f93496e93a8398/third_party/WebKit/Source/core/html/HTMLMediaElement.h

Verified in 53.0.2780.0 build.
Now Media option is displayed under settings after enable the flag (autoplay-muted videos)in about://flags page