While that's true, Morgana is, to put it nicely, batshit insane. She's also an advanced AI that knows how human reproduction works. So, in order to keep her man, she babytraps him. Lancelot however, doesn't have that option because he knows men can't have children.
Actually, if you play the straight path, Morgana is "unavailable" for the Holodeck missions, so Lancelot steps in instead as he's some sort of "back up" AI. So, in the straight path, they're two different programs. In the gay path, I imagine Lancelot won't shift back to Morgana, simply because Lancelot knows the MC loves him as Lancelot, so why would he go back to an "inferior" form that the MC has no interest in?
Firstly it's a contradiction to assert that Morgana changed into Lancelot for the Gay route, while defining Lancelot as a separate "backup" program for the Straight route. A more consistent way might be to imagine but programs as separate entities that had their rank adjusted (the Patreon code switching the Backup and Primary designations)... Do you still have Morgana active in the wrestling scene on the gay route? I'm guessing she doesn't manage the Holodeck missions instead of Lancelot on the gay route.
[For the moment I'm just going to write this of as an inconsistency that will probably get retconned at some point... and imagine the AI's as two distinct entities, Morgana & Lancelot]
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Isn't that moot, them being "different" programs doesn't change the fact they are digital constructs that don't have corporal forms, so any gender is purely a "skin", there is nothing stopping Morgana from wearing a Lancelot skin and vice versa. not to mention however the Morgana baby is made, it's not got anything to do with a womb/ovaries/eggs ...etc
I've avoided playing the last update (I want more story to build before I play again), but I do remember Lancelot, which is why I was surprised to hear you don't get Morgana on the gay route... I figured she'd rape you no matter what your sexuality was (maybe wearing the Lancelot skin to trick you

), though I'm not sure that would be necessary, after all she doesn't need to get you excited, she isn't using your sperm in the traditional sense is she, she's scanning your DNA or Brainwaves or whatever.
I gotta say I was looking forward to discovering what Morgana's baby is going to be! My top guess was always an android, but the more I think of it, some kind of tweaked clone is gaining traction in my imagination.
SO what happens to this Plot device on the Gay route if Morgana never raped the MC? Does she still get pregnant by some other crew member? (though that would be hard if she has had a "sex change" as you suggest.)