I think the easiest "fix" would be to elaborate a little bit on how the version numbers work. (Maybe in that first little paragraph at the top of the game's main page?)
I haven't seen any confusion yet for this game about it, but I have seen it a couple of times for other games that did something similar with their version numbers.
Viewing post in [BUGFIX INCOMING] Some Adjustments to the Rework comments
Oh shit. That's not a bad idea. My thought process is thus:
1.2.2.2
First digit (1) = the last season that I consider fully complete
Second digit (2) = the last episode that I consider fully complete in the new season
Third digit (2) = the approximate progress (main + side content) toward the finishing of the next episode
Last digit/two digits (2/20) = the most recent bugfix version