Yes, it's in the part where the actual ore separator is. You first need to trigger a switch or keypad on the upper level in sight of the separator conveyor. It opens a door with a vending machine behind it, making you think "why is that?". Then walk south of the seperator to the area where you would arrive if you use the mega secret shortcut. Just behind the health station towards the SW wall is a pressure pad on the floor that opens a secret door to the teleporter. Be careful, stepping on the pressure pad usually triggers a wallgun shoot rockets into your face.
The E-room is a big easter egg. It contains every weapon and item in the game (so you can get a full arsenal here including fusion battery and graviton shield if you have missed those) and a funny little cut scene in the room with the Pentagram. You will be "attacked" by a demon from Ultima VIII, but Tony Zurovec (the producer of Crusader) will appear and tell the demon he won't succeed, after which the Silencer will shoot the demon with the weapon currently equipped (doesn't take any ammo or energy).