There are a lot of good ideas here, but as others have stated the pacing and lack of focus prevent this from really coming together as a cohesive final product. General spoiler warning to the extent it matters.
Before I dive too deep, I at least briefly want to touch on presentation. I don't particularly mind the sketchy background and sprites - I think they come across more stylized than sloppy even if the appearances of our leads don't personally appeal to me. Similar to what another commenter said, the size/placement of Bianca's sprite looked a bit awkward in comparison to Artie though - less like she was meant to be significantly shorter than Artie and more like it was set to the wrong location on the y axis, like there was another half of the sprite that was sticking through the bottom of the screen. Didn't notice any major issues with the music, but this definitely could've used another proofreading run for spelling, punctuation, etc.
Last point in terms of presentation, again as another commenter stated, the switches between current events and flashbacks are abrupt and jarring. If you're switching back in forth through different points in time, you don't necessarily have to put a "20 YEARS AGO" title card each time, but maybe like a fade to black and fade back in, or a change in music to a consistent motif you use for flashbacks, or changing the color scheme between full color and grayscale, or a mix of the above could soften the impact a bit. Changes in time between "current" scenes could be conveyed better too - when we go to the cafe following the first flashback, Bianca asks if Artie still has a headache like it's directly following the first scene in the apartment, even though enough time has passed that Bianca is now showing. Either drop a line of narration heading to the cafe or have one of the characters note in dialogue that it's been long enough to tell Carter or something.
So, with all that said, let's talk about pacing and focus. As several others have pointed out, this VN moves at breakneck speed through all of its plot points, which prevents any of them from having the weight they need to really land. A great example of this is this line from the first flashback: "Why does my body feel bad? No I'm not sick... Why am I scared of puberty? Maybe it is normal... Why do I hate looking at my genitals? Wait... Whats trans mean?" Like, that's one line. We're speedrunning the entire trans discovery process in one line.
I think this is where focusing on the key themes and issues you want to get across could really help, even considering the limitations of the jam timeframe. Like ultimately we have a conflict, that conflict has causes, and those causes need to be addressed to resolve the conflict. As I read it, here's where this VN is currently at:
Conflict: Artie is insecure about becoming a father.
Proximal cause: Artie is not the child's biological father, as he is trans and could not provide the genetic goo to make the baby. This is fine - I can understand the insecurity regarding the biological situation on its own - the sort of disconnect between knowing the child is spiritually yours even if its genetic material is not (even if I think that should have been a conflict that was resolved before making the decision to try with a surrogate, not after).
Root cause: Artie's failed relationship with his transphobic parents (maybe). I think this is what you're going for, but this and the "biological" fear still seem a bit too disconnected.
Resolution: Unclear. After the awkward confrontation with Carter, Artie reiterates that he is scared, and Bianca says that they'll get through this together but that Artie needs to let her know what bothers him. And that's it. We get another flashback, and the next thing we hear from Artie is "Oh, I'm a dad."
I think it's worth considering if you even needed the flashbacks at all. Even if Artie's history with his parents continues to cause him to struggle with feeling like a "real man", leading to the present conflict, cutting the flashbacks in favor of actively discussing those concerns with Bianca solves several issues at once. The cause of the problem is more clearly articulated to both the reader and the characters that need to address it, and that gives Bianca a clearer avenue to then resolve the issue, such as by reminding Artie that he isn't his parents and walking him through some of the reasons that's true. I think this would also generally make the VN feel less rushed and disjointed with the frequent time-hopping.
I would also keep things focused to the one issue, and probably just to discussions between Artie and Bianca. The whole "intersex baby" plot that is introduced and resolved in five lines feels tacked on and unnecessary and the Carter confrontation scene feels out of place in terms of both pacing and conflict resolution. Like, imagine that scene from Carter's perspective: you show up to the cafe excited that you were able to help out your friends, then Artie spends the next five minutes panicking and getting angry at you for not understanding them, and then immediately leaves afterwards. Bad day to be Carter, I guess.
Overall, this VN had some really interesting ideas, but needed some stronger execution to really sell them.