Sure. The game has a light-hearted fantasy tone to it. Where the player is put in an absurd sandbox and allowed to do what they like with a lot of different girls and fetishes of the player's choice. So, why limit the player in this fetish? It seems more odd to limit what girls can be knocked up than to just allow it with all of them and let the player choose.
On the second part, I agree with you in that I think the pregnancy should not progress to full birth during the game. I think it should be resolved at the end of the game, during an epilogue instead. The player can still enjoy impregnation and pregnant sex in the mean time.
On to last part, it is a sandbox but the setting is at a vague fixed time. The player has "one semester" to save up money for school, find out why his dad was murdered, and find a date for prom. So, while the player doesn't have a time limit on an action, the action does have to occur in this vague time frame. Which is why I suggest any consequences of pregnancies should be resolved after the end of the game and maybe impact one of those goals in some way, but it shouldn't require a heavy story investment.
