In powerlifting, when performing a barbell squat, you are supposed to spread your knees apart and squat down in between your legs. This is proper technique and reduces the stress on the knee joint, transferring the load to the glutes and hamstrings.
I don't see why it would be unhealthy for you to do it without weight on your back.
I can't squat below parallel without getting pain in my hip joint and/or knees after a while. I am not built for low squatting, and especially not for going ass to grass. A lot of longer-limbed people can't hit full depth in a proper position.
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.
In powerlifting, when performing a barbell squat, you are supposed to spread your knees apart and squat down in between your legs. This is proper technique and reduces the stress on the knee joint, transferring the load to the glutes and hamstrings.
I don't see why it would be unhealthy for you to do it without weight on your back.