The additional girls [in Chemistry] will be ones who the player interacts with in future updates. Looking to try and focus on a few girls for interactions so that I can further develop their content instead of just a little bit of actions for everyone. Having the other girls show up later would seem odd as one would wonder where they were previously.
Yeah, the game is in-progress. No problem with choices that feel "missing" when that is exactly the case because they are part of future updates.
I will make a brief mention... many people want and or expect to be able to begin playing each updated version of a game by continuing where they left off. Sometimes that may not work. But so long as you are following the current trend of releasing a game in stages, this paradigm should be taken into consideration with how you choose to progress your development. For instance, continually changing/adding content to Day 1 only events with each new release does not really work. Even if you plan to work mainly on 1 girl only per release, you are likely best off spending as many releases as it takes to get all the setup of all characters done and then progressing by depth of individual characters afterwards.
Looking to have the player have at least some knowledge of the main girls by roughly the lunch period when he creates his journal so one has a listing of major girls. Wondering how best to address this as there are matters of player choice of class determines who he meets . And, like you mention, we don't spend every moment with the player through his day so he could very well have gotten a passing knowledge of the main girls. Text indications that the player gets to know who the girls are from classes. Running into the girls in the hall so as to cover ones the player might not have met through class selection. Something along these lines?
My personal preference would be that players do actually "see" the introduction of each main character rather than claiming some happen off-screen. Meeting people is simply to key of an event to claim it happened during the time the player is "controlling" this character but was not important enough to show. I do understand that tracking each first-meet can make for a lot of overly complicated code and tracking which shouldn't really be necessary. The easiest solution is to simply "force" all introductions. If you do feel like you really need to skip some introductions then I would suggest altering the story so that some preknowledge is actually expected (meaning some introductions could have happened prior to the time we first take control of the protagonist).
Examples:
First day of class actually has a full-school assembly. Key characters get introduced by the Dean, Principal, whoever is speechifying because they happen to be: head cheerleader, student president, champion athlete, leader of the chess team... whatever. Some that you don't want to promote to some leadership role can be sitting close by and get introduced or comments overhead during the production. Or one of two could even be bumped into on the way in or out of the assembly. That way everyone is introduced right up front and there is no wondering "when will a person finally first bump into someone."
Another option is to contrive the full first one or two days' schedule such that the player does not get choices of which classes to attend. Part of the agreement with getting permission to observe all the classes at random without committing requires that he attend all of them once first before he can begin choosing. And then he meets the girls according to the predetermined order of classes.
Or force accidental run-ins in the hall on the first day... Any random way you can think but if you want him to know everyone by lunch, then MAKE him bump into everyone by lunch. (You're the writer. If you want something to be true, edit the story until it is true.)
The other thought is when you say in the initial setup that Julia is now his only friend at school, change the script around at that point. Say that the player attended an Open House night at the school a few days ago. Or that he was able to tour the school a time or two in recent days prior to starting school. Or class registration required going to visit the campus. Basically claim even though he has never attended school here, he has been on the grounds a time or two. And claim that he did meet a few classmates during his visit. Don't name who he met. That way when a person is suddenly "known" without an introduction there is already a backstory in place as to how we probably found out their name.
