The overall height is different. The ER is 47.9" and the GT is 41.1". However, I think this is due to the windshield. The ER gets a mid-height windshield, the GT gets a low-height windshield.
So basically the difference is shocks. The ER gets the standard aluminum-bodied HPGs and the GT gets the piggyback clickers on the front and the Ohlins electric on the rear.
Hebi