While the set is important, it is a VERY good thing that you are concerned about BHS feet placement! Physics!! When your feet land in front of your body in a BHS, your next skill will travel in the same lateral direction and remain relatively low to the ground - so if you're doing multiple BHS, you want your feet to land in front of your body, so that you are in the optimum position to continue those long BHS skills. However, when you are using a BHS prior to an airborne skill, you want a long BHS where your feet land slightly behind your body (to be clear, this is for the BHS immediately preceding the airborne skill).
This is where I normally whip out my white board or piece of chalk and draw stick figures to help demonstrate, lol. The feet landing slightly behind the body in that BHS allows the rebound to direct the motion of the body straight up. So you're basically converting your lateral momentum to vertical, which allows for a higher set. You still have to ensure that your set is done properly, of course, but the angle of entry from the preceding BHS absolutely matters! (And your round off matters, too! An improperly completed round off can translate all the way through to your airborne skills, but you didn't ask about that so I won't go into further detail as I'm long winded enough, haha!)
I agree that you should take it back to tucks or layouts and assure that your BHS entry into those airborne skills is done properly. It will likely feel... odd at first, if you have been able to complete single full twisting layouts with a feet-in-front BHS. I would hazard a guess that you will be amazed by the amount of power and height in your set you will gain by using physics to your advantage.
Edit - I am always, always baffled by the number of cheerleaders with relatively high-level tumbling skills who have never been taught this.