This is no phenomenon. When there is muscle bulk getting in the way its pretty hard to impossible to do much about it aside from reducing it. Muscle bulk is a flexibility limiting factor simply because of the muscle mass getting in the way. Only real thing you can do (without reducing the mass) is to try to teach them (athletes) to relax the quad on the front leg to hopefully allow for the muscle to be displaced a little allowing for more compression.
it is common for the hip flexor to hurt in splits. its a good thing, it means they are maintaining pretty decent alignment in the split and are not cheating it (its an assumption made without actually seeing it, but it seems to me that you know what good alignment is so thus i make this assumption). When you say "pull the leg bent all the way up to their chest " do you mean with their arms or actively without arms. I would recommend that you add in your stretches a Thomas stretch kinda like in the photo
but you want to have the bottom of your glut muscle just on the edge of the table, and keep a straight leg. A partner can gently help by putting pressure on the middle of the straight leg thigh, while ensuring that the person getting stretched is keeping the knee into their chest, and both hips are down and they are trying to press their lower back in to the table.
The hips rolling at the bottom of squats can also be the result of
1- weak core
2- tight Achilles tendons
3- tight hamstrings.