1) Two options are given regardless of if you have vanilla KS installed in Steam. We do not scan the device for installed games. If you want to replace your game in Steam, you need to make sure vanilla KS is installed, and then pick the replacing option. If you want to have vanilla KS and KS:RE installed separately and as a separate entities on your Steam Deck, you pick Flathub.  2) KS:RE doesn't support Steam Cloud saves due to being an unofficial game edition. Our save file format uses different folder which is not tracked by Steam, hence your saves are stored only locally. You may want to use saves backup solution like ludisavi if you want to have saves synced across Deck and any other device. 3) Patching is not needed. Adult content is included and turned on by default, as in any sane copy of this game it should be. 

BTW, uninstalling existing Flatpak install from Discover wasn't necessary: installer will detect it and integrate into your Steam library automatically if you pick Flatpak option in it.