From what I understood from my research, -kun is more commonly used among boys, -chan is more commonly used for close girls or very close people in general, and -san is commonly used to demonstrate respect. If there’s any mistake in what I said, please correct me! The more I understand, the better I’ll write it!
This is kind of a “yesn’t” situation. Honorifics are status/vibe dependent and cultural context is so complicated that a lot of educational materials will explain it that way for simplicity, even when it’s not entirely accurate. In terms of formality and status, going from least to most formal, it’d be chan > kun > san > dono (in modern life this is for memes, jokes, or like historical dramas) > sama. In terms of grammar rules, these work regardless of gender…except due to societal shenanigans, gender ties into “who do you consider above/below you.” I’m not gonna get into all that though lmao.
The chan/kun gender divide is more of a little kid thing. For instance, in a lot of schools, kids are encouraged to start using -san around the 5th or 6th grade. Prolly more context than you need, but sometimes male teachers will even refer to girls as san and boys as kun, while female teachers might refer to girls as chan and boys as san.
As you get older, and especially in middle/high school, more teachers will start calling all students -san. But again, this is all flexible based on context. For instance, my Japanese teacher started calling me -kun instead of -san, once I had her 3 years in a row. Your coach might call you -kun, while your math teacher might call you -san. Some schools will even do -kun for boys and -san for girls for 7th and 8th, then do -san for everyone in 9th, but this is way too much detail for this explanation already and I am failing to keep this short.
Someone in a service role will always refer to you as -san or -sama, regardless of your gender. Ex: cashiers call you okyaku-san/sama, which means customer-san/sama. Usually depends how fancy the place is (sama is more polite). It seems a bit funny, but even a child will be called -sama at a posh restaurant, for instance.
In a work situation, you might call people below you -kun, people equal or above you -san. People above you can also be called -senpai. Unless they’re your boss. Then you’d typically call them by their job title. This is of course assuming a traditional company structure, because again…context.
Not everyone follows those rules though. You could use this to showcase a character’s personality. A flirty character might call someone they don’t know by -chan, even when social rules dictate he should call them -san. A flippant character might drop honorifics for everybody, even when it’s not appropriate.
The quick rule (for adults) is: anyone you don’t have a relationship with is -san. Whether you call them something else is based on context (how do you know them: work, school, etc.) and how close you are. But again, everything is context dependent and this just grazes the surface.
My suggestion is still to remove honorifics from gender selection, and instead give players a chance to pick their honorific once they have a certain % of affinity with a character.
Personally, I think it’s more cute if characters have different ones for players. Ex: A cutesy or tbh annoying character might call MC -tan, -pon, or something equally cringey. A more proper character might switch to First name-san instead of Last name-san.
You could even do a scene indicating the change where the character asks, “Can I call you MC-pon?” And then have a menu come up that allows the player to agree or change it.
This might be way too much work though, in which case -san for everybody works for the high school or older level, and avoids too many coding variables.
(I meant to keep this short, but it’s impossible. 
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