You can launch Opera with --show-component-extension-options to see some of the built-in extensions. One of those (maybe Google Hangouts) might be the culprit. But, none of them can be disabled, so you're out of luck. If it's not one of those extensions, it's something built in, so you're out of luck there too.
First of all, this is not solution - it's a workaround.
I'm using Opera 56.0.3051.104 on Xubuntu 18.04 but i think you can apply this on any other version of Linux DE.
You have to modify opera's launcher:
Right click on it, Properties, Pencil icon (edit the currently selected item), Command field (third from above) where opera %U is already written. Overwrite with:
opera --window-position=118,64 --window-size=1682,951 %U
That's actual settings for my 24' display and the Opera window is now positioned on the center of the screen in windowed mode. Of course, you can play with numbers (X and Y) until you get the desired position.
Hello. Finally it seems to happen to Slack and Rythmbox too. So I don't really know if is only an Opera issue or a system one. I'll try to reinstall MATE or the notifications library or whatever is involved in this thing.
I think the only long term solution to this problem is to actually compile from the sources and use the options that include Widevine and distribute that to Linux. I doubt Opera has any prioritised interests in this since it is a closed source browser
they are giving out no compensation.