I've had my Steam Deck for a year, and what I've done since I got it is simply install the RetroArch flatpak (via the Discover app), and use that as a front end for all my emulation.
It doesn't add emulated games to the menu, but frankly, I think I prefer it that way, and I don't have to worry about things contaminating future SteamOS updates - everything is silo'd away.
A similar option is doing this via RetroDeck[0] which is a flatpak wrapper around EmulationStation, which includes RetroArch, and includes several more emulators not included in the RA flatpak.
Going through the game UI has some advantages, like the Steam native controller rebinding for individual games.
All this tool is doing is adding a bunch of .desktop files in the right place and setting up the folders necessary for the emulator. It's not touching the root partition that gets updated with the rest of SteamOS.
I’ve spent a fair bit of time with EmuDeck and as far as I can tell, it doesn’t pollute your system install at all. It’s very lightweight. I wouldn’t be surprised to learn that it’s basically just a bunch of bash scripts that configure everything with sane defaults, plus a lightweight GUI.
I do the same. I like keeping emulated games separate.
I also add it as a non-Steam game to access it while in the Steam front-end and allowing for controller options. I'm guessing you might do the same too.
It doesn't add emulated games to the menu, but frankly, I think I prefer it that way, and I don't have to worry about things contaminating future SteamOS updates - everything is silo'd away.
It works great, I recommend it.