I'm glad you liked it :3 I would consider 1.0.0 to be the first 'final' version of the game - as in there is a cohesive story you can experience start to end without needing to wait on any further updates (1.0.0 probably wouldn't be the last update ever but just means that the main story is pretty much done) so just decided to start from 0.0.1 and count up from there there's no real meaning to it
And for MC.. I think he probably has picked up on a few things but resigned those to his subconscious and hasn't pieced anything together yet. Even in IRL it's surprising how unrecognizable people can become just by changing their outfit/style - let alone using wigs and makeup so it's not entirely surprising. If I start adding story acknowledgements too soon about MC seeing clues linking Vanilla and Katrina it'd become even more of "ughhh why doesn't MC just confront her already??" and I wouldn't be able to keep doing mystery NTR stuff... so it's up to players to interpret things as they wish until we do get closer to some kind of reveal scene.
And yes, there will be a different path more along the lines of NTS - but for now I am focusing on NTR which is the main route.