Yes, this is the final version. And it used to be distributed via patreon, until the Patreon administration forced the developer to remove Bardi from the game. Only after that the conditionally new version of Ep2 appeared, from which the developer removed (disabled) Bardi's content and fixed some bugs. But roughly speaking, yes - the only difference between Ep2 v16 on this site and Ep2 v16 on Patreon is the absence of Bardie and related content.
Read the
FAQ , it answers your questions. In particular, point 1.3.5. Regarding the "waitress", I can only guess that you probably meant blocking extra scenes in the latest version of Ep3 v12. If that's what I think it is, read point 1.5.12, there's an answer to that question there.
As for the patch bringing Bardie back to episode 3 (FAQ, 1.4.7), I don't know if it will work for Ep3 v12, the last version it definitely worked in was Ep3 v9. But essentially you don't need this patch, because no content with Bardie was added by the developer in episode 3. And the "return of Bardi in episode 3" is more for the fan - the ability to send Monica to him + some repetitive actions related to him. But no new plot for Bardie in episode 3 simply doesn't exist. So if you want to go through his content (Bardie, College), it makes sense to play Ep2 v16 (with Bardie).