Hey! I'm a dev who works on Student Transfer (under another synonym though)!
I wasn't there when Student Transfer started, only joining the team about 2 years ago, I think I'm somewhat qualified to answer :P
While not entirely out of the question that some unintentional inspiration went there, Student Transfer, which launched 2015, was inspired by another Visual Novel called "Press-Switch".
Press-Switch was, at least to my knowledge, inspired by all the Choose Your Own Adventure stories out there, not YAWYW in particular.
The Jon/John name connection mostly stems from the fact that both names are very common. We don't have the "John Doe" thing for nothing. Since Student Transfer is a visual novel which uses borrowed assets, having a tomboy red-head friend isn't a priority, you just look for sprites that fit the archeytpes (Tomboy, Cheerleader, Nerd, etc). Karyn and Katrina aren't that close in name that I'd say connection.
Bitchy cheerleader is also a common archetype and the names "Sayaka" and "Sarah" aren't that close that I'd call them inspired. Lots of female names have a lot of "A" sounds.
The sister connections are non existent though. Zoey and Holly aren't even the same character archetype.
tl;dr: While I can't disqualify any prior knowledge to YAWYW (would need to ask one of the founding members of the project), most of the commonalities don't go further than standard conventions in this genre. I mean, how many devices dropped from trucks/alien ships/whatever can we find in stories? Or magical books that do magic stuff? The tomboy/the cheerleader/the nerd are common archetypes. So no, YAWYW wasn't a direct inspiration for Student Transfer.