I have thousands of games across all PC stores and Galaxy takes a couple minutes to sync on my desktop, and it's much worse at 5 to 10 minutes on the Steam Deck and GPD Win, probably because the processors are slower.

I no longer want to use Galaxy as a unifying launcher anyway because most integrations still disconnect or crash all the time so it's more trouble than it's worth to me, and it's been years in beta

Unfortunately, even with all integrations disconnected and uninstalled, Galaxy still syncs all my games. Every. Time. I. Launch. It.

Is there any way to disable this auto-sync on startup?

Also, I know of alternatives to Galaxy, but haven't heard that any of them have full feature parity, meaning multiplayer, cloud saves and achievements

Are you, by any chance, running it on Windows 7? I had similar issues (slow import speeds, constant integration crashes, etc) when I ran it on my old PC but I built a new one this past December which runs Windows 10 and Galaxy both on an SSD and those issues all but disappeared.

No. The Steam Deck uses SteamOS 3.0 (Linux), the GPD Win 2 uses Windows 10, my desktop uses Windows 11. I'm very certain that it's the slow processor on these handhelds and the fact that I have thousands of games that need to sync every time for some godforsaken reason

Sorry for suggesting the obvious, but did you try to uninstall and re-installing?
You can also just remove those games from the Galaxy-Library, if they are not there, they can't be synced...

As for alternatives to Galaxy: you won't find a launcher that has actual feature parity because the features that you listed are generally not made available outside of the proprietary launchers of the various stores.
What launchers usually do (including Galaxy when it launches for example Steam games) is start the game through the launcher.
You can sort-of get cloud saves to work by using a savegame-manager and configuring the launcher to trigger a backup when the game is closed. But for all other features you'll actually have to launch whatever launcher the game/store uses first.

The issue was there immediately when installing Galaxy on the Win 2 and the Steam Deck. No point in reinstalling and it absolutely doesn't make the issue go away. It is the same on my desktop, the CPU goes hardcore I don't know how to do that. I don't think this is an option at all
And even if it was, I'm not going to remove 4000+ games by hand

Yeah, sure. I wouldn't delete 4000 games by hand either. But you can delete the database Galaxy uses to start from scratch, so to speak.
And just to clarify: Those 4000 games are not all from GOG, correct? Because Galaxy won't magically pick up your Steam-Account when it's installed. At one point you had to type in your credentials. If you don't Galaxy won't know about those games.

Do you know how I can delete this database?

And yes, like I said, those games are from basically every PC store in existence that also has a Galaxy integration. I think it probably also has quite a bunch of console games it picked up from the emulator integrations.

Also to be clear, I wouldn't feel a need to delete my data if it weren't for the forced syncing and excessive time and CPU usage every single time I start Galaxy. I'd really prefer to keep it if it weren't for that. I just don't think it's going to see a fix any time in the near future considering it's been like that for what, three years at this point or something

C:\ProgramData\GOG.com\Galaxy\storage
or just go nuclear and get rid of C:\ProgramData\GOG.com\Galaxy\ Well troubleshooting like this is kinda hard. I never experienced the problem you are having (I had about 3000 games in the library when I used Galaxy as a launcher).
But reducing the number of games in your library SHOULD help, even if it doesn't fix whatever the underlying problem is.

But this issue happens on new installations That's the thing really, I can't. They seem to save my owned games on their servers and redownload that list