I mean... The Enterprise is always doing questionable things with that deflector dish.
My head cannon says the Enterprise explored a wormhole to the Farscape universe, did a reverse gravaton beam on Moya, then immediately went back through the wormhole... And that's how Moya got pregnant.
Would also explain why all starships in the federation, after that point, were female (no dangly deflector)
The nacelles Make It Go, the saucer section is the head, and the neck is... Well, a neck. This is the OG enterprise, so it's old. And old people wear their pants high.
Therefore I submit to you that this is the only acceptable version, even if it isn't wearing shoes.
Going by the general design of living things (on Earth, at least) being a tube with appendages at various points, I'd say the first one is more likely.