At first I thought I agree with the post and now I'm second-guessing what OP is trying to convey. This is an amazingly ambiguous picture when posted without further commentary.
That last paragraph is on point. That's why I have two controllers at my desk, one regular and one Steam Controller! I love playing casual Civilization or XCOM on it and it's surprisingly great with some FromSoftware games, especially Sekiro (for no reason in particular, it just felt good and the touchpad worked without any issues).
Or more accurately: Finagle's law, often confused with Murphy's law. Murphy's law is more about UI design that shouldn't allow for mistakes. Finagle's law is about bad luck and the general perversity of the universe.
I just tried naively installing Diablo II from scratch inside Bottles and sadly I couldn't get it to work at all this time, at least not without further tinkering but I couldn't spare more time at this moment. I presume installing it like this and then adding it to Steam to use Proton could work. I know it worked for Warcraft III a few months ago. And then Proton usually handles fullscreen completely seamlessly.
If you're running RetroPie on a Raspberry Pi, it won't work there. Running it on a regular x86_64 PC shouldn't be a problem. Just install it through Wine (I can recommend managing it with Bottles) and launch it through Wine or Proton.
Right, I was too vague too. See my other comment please.