Clicking on external link opens a tab in wrong Chrome window The setup


2 monitors are connected to my Mac Pro 4.1 running El Capitan 10.11.4
Monitor 1 is a desktop monitor
Monitor 2 is a TV
My default browser is set to Chrome (Version 46.0.2490.71 (64-bit))




How I use the computer

I usually have multiple Chrome windows opened at the same time. At least a window for each monitor, but sometimes more.
When I'm watching movies/tv-shows and other entertainment stuff i use the tv and use the Chrome-window on the tv for stuff related to entertainment.
The desktop monitor is used for school/work stuff and researching different things, so i use the Chrome window there for that kind of stuff.

Problem scenario

Now lets say I have a Powerpoint slideshow or an email with a link in on the desktop monitor, and I click  that link, then a new tab would sometimes be created in the wrong Chrome window on the tv, even though i just used the desktop monitor Chrome window. 

How I normally work around the problem (in a less than optimal way)

I normally resolve it by right-clicking the Chrome Dock-icon -> Settings -> "assign to Desktop on monitor x", which will move all the Chrome windows to monitor x. But it's becoming a bit annying because i would have to setup the window size everytime i do this.

So I'm wondering if someone in here knows of a better solution to open windows in the "current" Chrome window.
Links are opened in the newest window, so the solution would be to open your media Window and move it to the TV first, then open another window for other things on your main display.

EDIT: When it comes to preference, I too wish there was a way to change this behavior. Opening in the most recently focused window makes sense to me.