Hi, Jeenz,
My son is also hypermobile and hypotonic and also detested having physio, which he had from 15 months old (when he could sit if put in that position or lie on his back, but not much else gross motor-wise, not even rolling over). He was not delayed in other areas, just gross motor.
The physio stopped when he was about 23 months, which was when we got him walking. Without the physiotherapy (and some piedro boots to support his weak ankles) there is no way he could have made so much progress so quickly (well, that and his obsessional practising, ploughing up and down with a cart until he had the strength to walk by himself). So, I would recommend finding another physio, despite the upset it causes. My son's physio was great - she couldn't get much out of him at the actual sessions, but she got to see enough to work out what he needed to be working on each month and she taught me how to do the exercises with him. So, effectively, I became his physiotherapist under the tuition of a qualified physio!!! A million times better than getting no phsyio input at all...
As for arm or hand flapping, this may just be something she has found that she can enjoy (if you can't walk, you've got to find other means of stimulation and entertainment from time to time!!!). It is sometimes commented on in children who are dyspraxic (problems with motor co-ordination), who have issues with sensory integration (over or under-reacting to certain stimuli - eg noise, heat, textures) or autistic, but is not part of the diagnosis of such conditions (ie it's not in the list of things a child must do to be dyspraxic or autistic), and can also be done by normal children as part of a phase they are going through which they grow out of, so try not to read too much into it, if that's your daughter's only odd habit!