Yeah, running non-steam games with steam proton works well. One way to do it is bottles.
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Does this work for games that I have in the EA App and Ubisoft-thingy too?
I can't say for sure, but the internet seems to think so: https://www.gamingonlinux.com/2022/03/heres-how-to-get-the-ea-app-on-steam-deck-with-bottles/
Adding non-Steam games has never worked well for me.
Another issue is that there is a database of tweaks Proton uses to make games work better, but I don’t think it uses it for non-Steam games.
Heroic with umu do use these tweaks.
I use bottles for other game launchers. You can select proton version once the bottle is created.
To add, is it bad to have all these running on one machine ? Steam, Heroic, lutris, will it cause issues ?
No, they don't interact at all. You can have any number of similar applications, and run multiple games from them.