I don't think it matters. Ponies constitute a single reproductively-compatible species, as demonstrated by Mr and Mrs Cake (both of whom are of mixed Pegasus, Unicorn, and Earth ancestry), as well as Cadance and Shining Armor (Alicorn and Unicorn, respectively).
This is the non-winged pre-princess version of Twilight. Clearly, before she left Canterlot, she magically made a male clone of herself, impregnated herself, gave birth, and left the adorable abomination in the care of the university's department of magical medicine.
Why would Twilight Sparkle's baby look like Twilight Sparkle? Unless Spike knocked her up.. otherwise wouldn't a pony sort of have the traits of the mother and the father?