The funny thing is that the first part of what you wrote reminded me how I had a ton of trouble intercepting, distracting, and extracting the escort tanks in "Traitor's Caravan", so I just decided "fuck it I'll go Nuclear on them" since I'd spent like an hour on this. So I dropped in with a tank and demolished them, but when I approached, the Skulls emerged. And the center of the camera's attention, the leader skull, jumped right into a hill, clipping through it entirely, and continuing its dramatic post landing stance.
It kind of threw me off that they hadn't accounted for that possibility, and it kind of ruined the gravitas of that moment. It was a good indicator of how they eventually appear though, at the beginning of the game the skulls are damn near terrifying, and you want to avoid conflict as much as possible. The first encounter, as contrived as the reasoning to first players to turn around is, it provided a very tense situation.
At first I thought their weapons were FAMAS' and was excited that we were getting all this weird phantom future tech like that and Sahelanthropus. I thought for sure the game would have some actual psychic prediction story point to explain this, like Sahel was developed based on not just Granin's research but Psycho Kiddo's visions of the future. The best way to capitalize would be to eventually bring in primitive Gekko enemies now that I think about it, something completely foreign to the characters, but enhancing the mystery nicely. Though I hadn't though of it at the time.
But yeah, the Skulls could really have been a really amazing boss unit, but since they don't have any characterization or even squad leaders that distinguish between the horde, they are just kind of another wasted story element. I thought it was also strange how they never explained why Skulls were like Cyborgs but Quiet wasn't, and why they seemed like more "complete" Skulls, except I guess Skullface let Quiet look less like a corpse to get Venom's trust.