JSGME works for any game that follows a set/definable folder structure and substitution of files.
JS will have more thoughts on this but you could potentially combat the Ubi 'always online' Auto-patch by having JSGME auto disable activated mods after each play session. While this doesn't stop the patching altering file sets, it does leave your mods intact.
Then there is the question of compatible save files
. Lets say that you finish a patrol with X, Y & Z mods activated. That save file is updated/saved on Ubi 'death star' Server. JSGME disables all your mods. The following day you return to find that an automatic patch is required for continued play of SH5, fine you do so. Game launches and downloads/syncs your last save file.......SAVE FILE CORRUPTED!!!!
Thanks to Ubi meddling our Mods and latest Save state is of no use.
Whether JS wishes to go down the route of JSGME 'demagnetised my fridge magnets' is anyones guess. I'd imagine that he had enough of that with Commander.
Worst case scenario, but it'll be amazing if anyone even bothers trying to mod for this game until the tether is removed.