Also:
1. the icon badge color is blue instead of red
2. the icon badge text is too small and not middle/center aligned
3. there's a 1px gap to the right of the toolbar

Can confirm on:

1. Linux stable(!) Version 51.0.2704.63 (64-bit) / Ubuntu 14.04 (no flags)
2. Windows Version 53.0.2751.0 canary (64-bit) / Windows 10 (no flags)
3. Windows Version 51.0.2704.63 m / Windows 10 High-DPI (with flag enabled)

The major problem is that it spilled into Linux stable, and setting the flag to Non-Material has no effect.

Regarding badges (and not icons themsleves): https://bugs.chromium.org/p/chromium/issues/detail?id=612748

This is a planned change.  crbug.com/546206 

This change made the icons less legible:

1. a lot of extensions won't be updated to have a 16px icon so a distorted scaled-down version will be displayed.

2. a 16x16px icon is too small, there's too little space to include nicely drawn details so many icons will look alike.

3. since the icons are small and the overlayed infobadges cover parts of the icon there will be many users who have similar looking icons, so they'll have to examine carefully before clicking the one they need, losing their time due to bad design.

Whoever pushed this change didn't think it through or had faulty reasoning (probably something ludicrous from a user point of view like "simplifying of codebase" or "simplifying requirements for extensions").

Issue has not been modified or commented on in the last 365 days, please re-open or file a new bug if this is still an issue.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot