I don’t know of any extra benefit to performing EMS in the stretched position only that it seems to make it more tolerable.
I typically use EMS on the hamstrings while in the good morning position purely for comfort reasons. Just try using EMS on the hams while in the leg curl position! The pain is unbearable and it feels like the muscle is going to get ripped off the bone!
Also when using it on the quads I would recommend locking your foot behind something, otherwise it feels like your leg is going to snap!
This is all assuming you are using the device at high-maximum intensity as Charlie recommends.