My son was about 38.5 inches when we last visited and he was measured twice on 7DMT almost every time we rode. Never bothered me, though one time he was all slouchy for the second measurement and the cast member was using some phrase my son had never heard to get him to stand up - finally I told him to see if he could bump his head on the device without going on his tiptoes and that worked. I think he was trying to avoid his head touching…
Also, I can see the point of having two measurement stops as the first stop is also where people have to scan in for Fastpasses, get rider swap lanyards, and direct all general questions and complaints so those cast members are busy and it would be pretty easy to just rush your child past.