That has just always been the case as long as the app in both stores uses the same package string. (Like org.blitzortung.android.app or org.videolan.vlc)

Could be, but that could also just be done locally. Like your phone checking the apps you have installed and seeing if the same ones are on the play store. Having an install limit for an app - assuming that means that the app can only be installed some total number of times globally (a local install limit wouldn't make any sense I think) - necessarily implies that when you install an app through an APK, it has to tell Google that you installed that app so it can track how many people have installed it and not approve installation of the app if it's over whatever the limit is.

I think that's how it works when you have apps with the same name from different app stores, I noticed it with a different app like two years ago.

That's interesting. I was just checking to see if Cromite showed up there but couldn't find it, is there a menu you found yours under outside the update tab? If something as simple as a browser I use is going to be blocked from installs/monitored I can't see why I'd stay in this ecosystem.