Let me jump back in with this one suggestion, and I'll make a Mantis if you feel it is something within the realm of possibility. I obviously am one of a few who like to have my game universes in my pocket, and with this game's updates tied to Steam, this hamstrings me a bit.
What I can personally do to resolve this is go back to my home machine, update the base installation there, and use synching software like SyncBack to copy over the new/changed files to my drive, without wiping out my saves or settings. It's a hassle, but a fairly minor one.
Would Arcen consider a midway for this use case: an executable, a "Bionic Dues Flash Packer," that comes with the Steam game. When you run it, it asks for a location, then copies the game files to that location, updates them if they are already there, and doesn't wipe out saves, settings, or any other user files?
I'm no programmer, but this might be accomplished with something as simple as a batch file or an AutoHotKey script converted to an executable.