No, actually.

Your game files do not need to be inside a prefix, and I generally do not set things up that way.

Same as on windows you can have your c drive, but then install games to a different drive. You can mount any file location as an additional drive in wine. There is usually already a "z" drive mounted, which gives the prefix access to the filesystem outside the prefix.

This means there's not actually any need to place things inside the prefix, except for save files which need to be in specific locations like appdata or documents.

So to move things over and run them, you'd just copy the game files anywhere you like. To run a game, instead of a location on the c drive, you'd use the corresponding z drive path to the exe.

With bottles, this is super easy. Set up a bottle, and copy any save files into the prefix. Easily done with "browse files" from the config page of a bottle, which will open the fake c drive in a file browser.

With a configured bottle, simply navigate to the game .exe. Right click it, and select run with bottles. Bottles will ask which bottle to run it with, and that's that. Alternatively, use the "Run executable" button found on the config page of the bottle. For ease of use, add the exe to the bottle as a shortcut.

Shortcuts can then also be added as start menu items, or even added to steam.

No need to fiddle with putting all the game files inside the fake c drive.

Setting things up this way means you have your prefix, with save files and such, separate from the game files. You can easily delete or add games, without touching the save-file-containing prefix, and move games around to wherever you need and still have them work.

You can re-use the same bottle for many games, and keep the save files for those games in one prefix.

If a given game needs a bit more massaging to work, bottles makes it very easy set up and manage additional bottles for any such games.

If they are all installed in the same wine prefix you could back up everything in one go by archiving the ".wine" folder in your home. that will include all applications installed in wine and all settings for those applications.

if you want to separate them into one archive per app you should look into wine prefixes, otherwise you would need to identify every folder a given app created during installation and archive those together manually, which can be very tedious.

I use Lutris and set up my directories a "GameName" and then 2 subdirectories "game" "prefix" and point Lutris to these.

All of the game files go in "game" and the prefix is created in "prefix" when I press play in Lutris. Any extras dlls that are needed can be installed with winetricks within Lutris to that specific prefix

This way you can just compress and decompress "GameName" folder and point Lutris to these locations on whichever machine.

You can choose which prefix version you want in Lutris and it will download that version for you. ~~I'm pretty sure it saves the version to somewhere in ~.local/share/lutris I'm not at my PC now so not 100% sure of the path.~~

It saves it to ~.local/share/lutris/runners/wine and you can put a custom wine build here and Lutris should recognise it when configuring the runner options

So you could copy this over to the corresponding location on the deck and Lutris will automatically detect this version as installed and won't have to download it again but its not necessary unless you don't have internet on the deck, or you're like me and want to keep an archive of the working prefix for the future in case the prefix version is no longer available for whatever reason and other version just won't work.

If you're new to Lutris, I wrote a step by step guide on how I use Lutris on a different community

https://sopuli.xyz/comment/9858101

I understand that with wine/proton prefixes they should be installed to a “fake c:/ windows hierarchy” can I just compress that and copy to a different Linux machine?

Yup, your save games are in your wine prefix so feel free to back them up and just use them again. Note that the game itself isn't necessarily in the prefix, you could have installed it elsewhere.

Does it save which proton version was used?

I don't think so, but it shouldn't matter. You can change versions any time and it'll just update your prefix.

If I use something like Lutris or bottles can I import into them?

Yes, you can set the prefix path to that folder you copied and it should pick up where you left things.

rsync

Lot of great answers. Must save post for Linux newbies. If you play native linix games their saves will most probably in /.local/share/ or /.config. If you use repacks like jc141 they have their own prefix in /games/jc141/.