I just want to try and allay your fears a little about your daughter possibly going to a school without her best friend.
I have a daughter who is EXTREMELY anxious and I was VERY worried about the transition to secondary school (and so was she). I and our primary school SENCO spoke to the secondary school's SENCO before she started so that they could be aware BUT it could not have gone better (and the SENCOs didn't have to do anything special). And all the schools I am familiar with do a lot to help the transition.
Also, best friends (even the strongest, apparently life-long best friends) in primary school simply may not remain best friends in secondary school with lots of new people and completely new social dynamics. The best friend may not be in the same class etc. And that can be even more devastating to the child who finds their 'best friend' moving away from them or making new friends.
I really really wouldn't choose a school on this basis and I would spend time reassuring your child that she will make new friends and that everyone will be in the same situation as her.
I would second that! DD started Yr7 last September at a school that we had not even listed on our CAF, and although she was originally one of 5 from her primary allocated to that school, in the end she was the only one who actually went there (although one boy was still officially there come September, but never actually went). Her primary school best friend got a place at a semi-selective school several miles away in the opposite direction. Occasionally, DD gets a text to say that "PSBF" saw her waiting at the bus stop as she went past on the bus on the opposite side of the road that morning
But they are still friends, and still meet up and skype each other. DD was actually glad that none of the other DC from her primary school went with her to secondary - they were none of them particular friends of hers and I think she worried that others would expect her to want to be with them, especially as the secondary school intake consists mainly of large groups from Yr6 at 3 primary schools the other side of town from us. She now has a new group of friends, and they all also meet up and skype etc. Awkward moment one weekend in town with both PSBF and SSBF when DD felt that they were going to go off without her, but it all came out in the wash, so to speak...
DS1 went up to GS with only one other boy from his primary, not a particular friend either. He now seems to keep up via Facebook with kids from primary I never even thought he was friend with either