The display configurations are intentionally different.

Endeavor will be displayed as a full Space Shuttle stack(with ET and SRBs). "pre-launch"

Atlantis is displayed as flown in space, with payload bay doors open. "during mission"

Discovery is displayed as just landed, landing gear touched down.

Enterprise was never fully an Orbiter/Space Shuttle, but it is displayed on the Intrepid using the mounting joints that connected it to the Shuttle Carrier Aircraft (747-100).

Challenger and Columbia we of course lost in two separate accidents. There are memorials across the country, but at KSC right below Atlantis are a piece from each Orbiter on display.