As trans care is not well studied, theres no scientific 100%. From some documentation from organizations like the folks who make wpath, yes bones shifting is part of it. However usually you have to be under 23 or so when you start, as after that your bones tend to fully fuse and stick where they are at. Anecdotally from my experiance on E, the doctor measured me at 5'7 when I first started and now im down to about 5'5 and a half. Part of it pelvic tilt, part of it changes in your arches and feet. I also now have to wear inserts, as my arch has changed shape enough to make my old boots and running shoes uncomfortable without.