In general, as an embryo grows the body plan expands forward/upward (rostrally) and backward/downward (caudally) from the bottom of the brain. The area of the top of the neck/ bottom of the brain could therefore be considered a starting point, a ground zero, once the embryo has curled into a three-dimensional form: Certain structures are built there and drop down later, like the heart and diaphragm and beginnings of the gut, while the brain grows up from there.
It is useful to know first, that the brain develops medial to lateral, growing up and forward from its floor and expanding/falling outward to the sides: I propose that the homunculus is a mapping of developmental biology: As the 'unfoldment of the antigravity suit' proceeds out in the periphery, its progress would appear to become “registered” by homuncular “maps” of the body in the central nervous system. Picture the homunculus diagram draped over the cortex; think of travelling along the homunculus from its oldest represented body part on the outside bottom part, up and around to its most recent represented body part deep inside the medial sulcus.
As the gut tube starts to form, the anus end (proctodeum) forms first, then the mouth end forms (stomodeum) and a curtain is dropped down right away to separate the two; the rest of the gut will be built over the next several weeks, and these two end zones that are already in place will become widely separated. If you look at the cortical homunculi the anus is there on the outside of the brain, in number one position, the first (and most lateral) place, 'under' the number two part, the pharynx. The genitalia, bottom of the trunk, and legs form last in the embryo. We see the latterly formed body parts represented inside the medial sulcus. Embryology can help explain why anus and genitalia representations are so far apart on the cortical representative maps.
Anus is ectoderm, and has an obvious place in the sensory cortex. We need to be able to "sense" the process that happens there, and have some sort of conscious motor control of it, so that we can 'hold it' until we're not busy with something else. It likely evolved this way for all sorts of predator/prey, ‘waiting until we got away from danger’ sorts of reasons; however convenience is certainly an important feature in species that are as social as primates and humans, and appreciated in our companion species, e.g., dogs.
Next to develop is the neck and head, a big investment of time and embryonic resources. The neck, throat, mouth, face, rostral sensing apparatus (eyes, ears, nose, tongue), swallowing and breathing parts have to be built right, or survival will be drastically curtailed. Hence the throat and big lips/tongue/face on the homunculus, right after the anus.
At the 'top' of the brain maps are found the trunk and arms. Developmentally the hands poke out the neck zone first, and develop thumb first/little finger last. Then the arms grow longer, distal to proximal. All of this appears in proper sequence of ordinary depiction of the homunculi.
The trunk takes up little space on the homuncular maps. Why?
Anatomically a lot of trunk, the spine at any rate, (both representatively in the homunculus and anatomically in the actual body) is "covered up" by or overlapped with lats which are 'arm' muscles and traps which are branchiomeric (from the neck or cranium) muscles.
(I can't help but think it must be a bit confusing for the motor homunculus when the sensory homunculus has input from little dorsal cutaneous branches sticking out to the surface of the back, feeling the environment just fine, but the muscles that are run by the motor branches of those same nerves are buried completely by superficial sheet muscles. Could that be why back pain is so common?)
Legs come later after arms. My theory develops a problem here: I'm not sure why the knees are depicted curling around the central sulcus; feet and genitals are depicted close together, but feet come some time prior whereas genitalia is last to develop along with the thighs.
The feet actually form before the legs do, two little feet sticking out of the sides of the trunk with some primordial gentalia beween them. Then the feet shoot out from the body, carrying the peripheral nerves with them, and the legs grow to catch up, distal to proximal. Their representation is always shown down inside the sulcus. Perhaps the gentalia belongs there as it develops last of all, but I think on the homunculus the legs/knees should come after the feet, not before.
For my little theory to remain consistent with reality, more advanced future mapping will have to show arms and legs depicted as telescoped concentric rings, maybe ovoid, with the hands and feet in the center, all the rings touching on the lateralmost side. I would expect the representation of genitalia to be overlapped with the thigh representation, the medial side only.
In summary, the representations make more or less embryological sense just as they are. They can be reasonably considered a map of the body in the logical sequence in which it selfbuilds /unfolds, in both the classic sensory and motor cortical homunculi.
Motor activity is believed to be present before sensory pathways are built, so the sensory homunculus either may take its cues from the motor one right from the time of the unfoldment sequence, or possibly a lot of it is hardwired right from the start and simply awaits myelination.