I've run into issues where a game will work with a specific version of wine but then not work with a newer version but then other games that don't work with the older version, work with the new one.

Theres also potentially issues of dependencies for one game breaking another game. Separate prefixes just make it easier to troubleshoot a game not working since you can just install/uninstall whatever dependencies that it might need without worrying about messing up other games.

Its also just easier to delete the entire prefix when you realise you've installed too many useless dlls and you've finally found the one thing you do need to make the game work lol

I also like to archive games I like since companies can just decide to remove their games from existence whenever they want. So I just add the separate prefix that has any extra dlls or tweaks to the archive so that the game should still work in 3 years without having to try and download dependencies that may not be as easy to find in the future

But if you don't have issues I don't think its a big deal and if you do have issues with a game, you can just make a separate one for that anyway.