I have long femurs as well and can't squat comfortably for very long periods of time either, it feels like it cuts off the blood flow in my knees, but I would argue that that is most likely due to years of adaptation to a life of sitting on chairs and sofas, rather than due to some hereditary physiological quality. The more I squat and the more I get used to squatting, the more comfortable it becomes. When I started powerlifting, I struggled to hit depth, but now I do go almost ATG on every rep without any discomfort in my joints.

I really don't think there's any bone preventing you from squatting to depth. I believe it's almost always an issue of the condition of your muscular and connective tissue.