Using Tiled, you would place down tiles which your game engine would translate into the appropriate “3D” modules (floor, ceiling, walls). The actual modules used by the game would not be previewed in Tiled, Tiled would just be a layout tool in this case, nothing from Tiled would be directly visible in-game.
Edit: if you don’t want to program room modules into your game, you could have six layers in your Tiles map instead (Floor, Ceiling, each of the four walls), and your engine could take the tiles from those layers and build the room out of them. If a room is missing one of more of these (e.g. the North wall layer is empty for that tile), then that means there’s a passage that way, which would allow you to have adjacent rooms that aren’t necessarily connected. Or you can just base the passage stuff on the Floor layer alone and just grab tiles from the other layers as needed (that would probably be easiest from an editing standpoint).