Vaginoplasty is the surgical creation of a vagina. I think you mean vaginectomy, which is the surgical removal of the vagina. I am going to respond to this as if that's what you meant, because it doesn't make sense to me that you would be wanting a vaginoplasty.
During phalloplasty, the clitoris is either buried inside the base of the phallus or is slightly left exposed on the underside of the phallus just above the scrotum. I've seen it done both ways by multiple surgeons. I'm not sure if it's a matter of technique or patient request, so if the positioning is important to you I would be sure to ask about it in a consult.
With what you're describing, the vaginectomy would close any opening down there aside from potentially the urethra. If you chose to have urethral lengthening to the tip of the phallus, your urethra would be re-routed. So no holes down south. The scrotum is created from the labia majora. The ligaments around the clitoris are released, and it is positioned as described above. And then the phallus flap is placed over top.
I'm not sure how, if at all, that would impact the internal structure of the clitoris. Many surgeons require a total hysterectomy pre-bottom surgery. If you want urethral lengthening done, a lot of surgeons will require a vaginectomy. After the first stage of bottom surgery for people who get those things done, the only reachable part of the clitoris is if they've had it left exposed above the scrotum. I'm not sure if the release of the ligaments around the clitoris do anything to change how much of it is visible.
Every guy I know who has had phallo has at a minimum sensation in the base of his penis where his clitoris is buried, and even guys who opted out of microsurgery or chose flaps where that wasn't an option have that sensation. I think regardless of what you'd have done, your sexual response would be different. There's a relearning period.
