UserAgent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.87 Safari/537.36

Steps to reproduce the problem:
1. Open two separate Chrome windows, call them window #1 and window #2
2. In window #1, type in the address bar "javascript:alert('test')"
3. Click on the address bar of window #2.

What is the expected behavior?
The address bar in the window #2 should receive the input focus

What went wrong?
The alert box in the window #1 blocked the focus.

Did this work before? No 

Chrome version: 56.0.2924.87  Channel: stable
OS Version: 
Flash Version: 

This bug was reported before here
https://bugs.chromium.org/p/chromium/issues/detail?id=3658
but I think there was a misunderstanding that resulted in closing it.
First, this behavior is different than Firefox. I tries the same scenario with two windows in Firefox and an alert box blocks only one window.
I am fine with an alert box blocking all tabs in one window, but blocking other windows is too much.
This error becomes more serious if you use multiple desktops or workspaces. I do this in Ubuntu and I usually keep Google Calendar, for example, open in one window in one workspace. Whenever a notification pops us, I suddenly lose the focus on all open chrome windows on all the workspaces and the workspaces automatically switches to the window with the alert which is very annoying. I started to experience this problem only after I switched from Firefox to Chrome.