Yes, force the compatibility to Proton Experimental. You can try without the launch options and see if it works. Keep a copy of the launch options just in case though.
Yes, its fine to have your OS on a separate SSD and use your HDD as data storage.
Its also important to maintain your drives. Be sure to have SMART alerts, and do spinrite or badblocks occasionally to let the drive firmware remove bad sectors from use.
Oh, never met anyone that despises their own data. Hell yeah, dude. Lose that data!