Ironically we just had our letter today confirming that Peter has Ehlers Danlos III! Also in the letter was the round up of that days observations (we had previously seen 'a member of the team' dr and this time it was the chief paedatrician so she wanted to see for her self) and it says:
Peter has signs of generalised hypermobility but with tight hamstrings and very poor muscle bulk.
During the appointment she actually commented that it sounds counter intuitive but tight hamstrings are very common in hypermobility. And they are actually a lot less tight than they used to be! In fact besides the pain in the ankles and feet it was the tight hamstrings that made me first see a physio. She got us to make a sort of wedge out of Lego to put under Peter's knees as he sat on the floor with his legs in front of him to watch TV and to lower the height of the wedge by one lego block a week. It took months but we got there in the end and he can now straighten his legs again, and hasn't had to keep doing the stretches over the wedge.
The tight hamstrings was explained to us this way. When the bones grow, normally the tendons are strong and they keep their length and cause the muscle to stretch and grow too. But if when the long bone grows the tendons stretch instead, the muscle doesn't have to and will be shorter than it should be.
So if someone is using the 'can they touch the floor with their hand flat' as a criteria, rather than actually understanding the structure of HMS, then they might think that tight hamstrings means no HMS.
I hope you can get a second opinion with someone that knows more about this!