The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/d7115b681d0852f64676445b13f50f026f111e71

commit d7115b681d0852f64676445b13f50f026f111e71
Author: lgarron <lgarron@chromium.org>
Date: Tue Mar 07 02:40:39 2017

Cocoa Page Info: Take built-in padding into account for "Site settings" button placement.

BUG= 698466 

Review-Url: https://codereview.chromium.org/2723233006
Cr-Commit-Position: refs/heads/master@{#455025}

[modify] https://crrev.com/d7115b681d0852f64676445b13f50f026f111e71/chrome/browser/ui/cocoa/website_settings/website_settings_bubble_controller.mm

Is this fixed now?

Yep!