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you'll just use your PC to make your mod set, do all the optimizing, LOOT sorting, etc, then you'll move a static copy of your MO2 instance image over to the Deck, basically making it a manual mod installation...
so MO2 has a file browser built-in to it, you pick it from the executables drop-down tab for that given instance... it'll mount your VFS image, and let you see inside it, and manipulate those files.
so either make a temp directory to hold it all, sure it can be a flash drive but hopefully it's a fast USB3 and big enough to copy all of Data\ at once, or just directly map your Deck's storage as shares in Windows via SAMBA, and from inside that MO2 file manager, you'll go into Skyrim Special Edition, and just copy the entirety of Data\ to the Deck's copy of Skyrim, you'll then go into $APPDATA\Local\ and grab the Skyrim Special Edition directory and put it in your Deck's proton prefix which is compatdata/489830/pfx/drive_c/users/steamuser/AppData/Local/ in Desktop mode...
you'll need to reinstall anything directly into Skyrim that was handled before, like SKSE Reshade ENBs etc depends on what you are using... SKSE is easy you just extract it, proton/wine is smart enough if it exists, it uses it, no configuration on your part.
any modded saves that go with this modset can be copied too, of course, destination path will be compatdata/489830/pfx/drive_c/users/steamuser/Documents/My Games/Skyrim Special Edition/Saves/... copy the last 3 or so whatever ones you really want to bring over. (do NOT copy the whole Skyrim directory here, that will bring over your configuration files, your error logs, etc, which are going to be specific to each machine, leave everything but Saves/ on the PC.)
as long as the Plugins.txt file exists under AppData\Local\Skyrim Special Edition\ it'll know what to load in what order, and as long as the mods actually exist to be loaded, you'll be fine. and if you bring a save with you, you'll be better than fine.
when you want to change your mods, do it on the PC, then tweak and tune and re-run LOOT, and when it's happy, repeat the steps.
sorry it's a little bit technical, it's a very cool 15W little linux handheld laptop afterall. but easy peasy!
if you're a visual learner I'm sure some industrious person made a video or 6 explaining this.
happy mod cloning!