We were in a very similar situation as you. DD1 was accepted to one school and waitlisted at others while her twin was waitlisted at all and, unsurprisingly, didn’t get off of any waitlists. Both required FA. In the end, DD1 went to BS and DD2 went to LPS. The next year DD2 applied to the same BS as her sister and was accepted into 10th grade with FA. While there was a little friction during that first year, it was manageable and the girls actually grew closer by being at different schools. At the end of the day they’re different people with different strengths so sometimes one person “wins” and the other person “loses.”
The difference between this and making a sports team or an honors society, or whatever, is the money. I don’t know what level of FA you need to make it happen but unless it’s a full ride there may be some hard feelings about that aspect … “we’re spending $x,000 to send her to school and now we can’t afford to go on vacation.” You know the dynamics of your family best and whether or not that would be a problem … or perhaps a teaching moment.
Regarding the schools, it’s already challenging to get off the waitlist but even more so when you need FA. Because of that, I wouldn’t put any barriers in place if you really want one (or both) of them to attend. Be honest with the school. If you’re okay with just one getting off the waitlist, tell them. Just recognize that only one may be at BS. If you must have them do the same thing (both at LPS or both at BS) then just tell the schools that.