Meta-progression (which Upgrades you've unlocked) and settings (resolution, volume) now carry over between devices!
But heed these warnings:
Cloud Storage works fine with the Steam Deck, but the Deck only pushes data to the cloud when you quit the game, not when you put the device to sleep.
If you use two different Steam accounts on the same device, they will use the same data: same meta-progression and same settings.
Mid-run progress (as opposed to meta-progression) is (still) not saved.
There are solutions to (1) and (2). But those are a bit more complicated to implement, so I'll defer them until a few people ask for them on Discord/Bluesky/Forums.
There are also solutions to (3) but that's a BIG lift and each run is like 5 minutes long anyways, so that's probably fine!