I’m also an EDS-diagnosed rider in my 30s. I’ve had similar problems in the past with my lower leg bunching up. I think part of it IS making sure the horse is properly trained to respond to your leg - if you are constantly nagging, your heel will tend to come up. But I seemed to have a harder time than most people.
The things that have worked best for me:
First, PT, PT, PT. You have to find a PT who understands EDS and can identify the best areas to target in order to stabilize you. And they need to be able to ensure you do them correctly and progressively. For EDSers, this is harder than it sounds! It is so easy for us to miss strengthening smaller stabilizer muscles and just fling our weight onto already-overdeveloped muscles–or worse, our joints.
Second, try to stay in the best shape you can, include as much resistance/weight training as you safely can, and try to find forms of exercises that complement your PT strengthening goals. For me, this mean working a ton on my core (especially the deep stabilizing muscles) and posterior chain (glutes, hamstrings). And cycling is really helpful, because it stabilizes my pelvis and works some of the muscles along the base of my spine in a way that’s really good for me. EDS sufferers also tend to decondition really quickly (the pandemic shutdown was ROUGH), so be mindful of that and try to avoid long layoffs unless you have an injury.
Third, just in terms of my riding position, doing lots of two-point is really helpful. So is practicing balancing at the walk while standing in the stirrups. No-stirrup work can be a double-edged sword, because it tightens my inner thigh muscles and that actually throws me pelvis out of whack. Doing PT right before/after riding is also fantastic - a little bit of glute/hamstring work reminds my body to use the right muscles in the saddle, and some abductor exercises and adductor stretches afterwards helps rebalance my hips/pelvis and lessen the anterior pelvic tilt someone else mentioned above.
and going to try some workouts.
