Hi,
I recently got Blasphemous. I played it on the deck for an hour, and then when I booted it up on my pc, the save file didn't exist, because the linux version and the windows version of the game apparently can't share save files. So my playthrough is stuck on the deck.
If this is the case, and with the existence of the proton interpreter, Why would I bother with making a Linux version for a game targeting the steam deck?
It's up to the developer to set up steam cloud saving properly. It's definitely possible to share save files between different operating systems, i've done it myself. This has nothing to do with the export option, with Auto-Cloud, the developer must configure the save path mapping correctly across OSes, using a single root plus overrides for cross-platform sync.
A proper export would surely run smoother than letting Steam run it through Proton, so there are surely some benefits. Possibly a little quicker to get through the SteamDeck verification process as well. The game would also be listed as "Native" on databases like protondb and so on. So marketing wise it might do you some favors too.
However again, this has nothing to do with cloud save syncing issues.
If you as the game developer use Steam's Auto-Cloud feature, and want to support cross-platform saves, then you must configure a "Root Override" for each OS manually within Steamworks. So it's possible that they missed that on Blasphemous if what you're saying is true.
For more details, checkout the "Cross-Platform Saves" section here:
partner.steamgames.com/doc/features/cloud