So I just took Seltkirk's armor off of Traut, including a key, and all the way to the right is a door that requires a key, obviously not Traut's key or it would have opened. Does anyone know where I can find the key to this door?

There are two entrances to the room behind the locked door. The key opens the other one, which is the entrance through the Tower of Debauchery.

There's one door that leads up some stairs and you exit at the mysterious merchant. I believe the key opens that door. I don't care about that door.

There's a second door all the way at the back of the room, right of where you entered via the trap door with Whistling Wendy. I want to explore the area behind that door, but I need a key for that. I want to know where the key is.

You're on Roche's path, and that door can only be opened on Iorveth's path. It'll have to wait for a second playthrough.