Yeah, that should be possible, too.
The generator doesn't use any special data structure to store the generated level. Everything is done with built-in Unity tilemaps (https://docs.unity3d.com/Manual/class-Tilemap.html). So if you get the instance of the Tilemap class, you can call the GetTile method to see which tile is used in a specific position.
Example usage:
1. Define room templates as usual using 2d tilemaps
2. Let the generator create a 2d level
3. Create a post-processing script that gets access to the output tilemaps of the generator
4. Go through individual tiles in the output tilemaps and spawn corresponding 3d tiles
5. Do some cleanup (hide original 2d level, etc.)
This approach would be very close to the normal approach, just enhanced with a custom post-processing logic. One theoretical problem with this approach is its performance. The generator will compute things that are meant for 2d levels and you would then discard them and replace them with a 3d level. You should definitely avoid doing one thing - recomputing 2d colliders for the output tilemaps (assuming that you don't want them). This is probably the most computationally demanding step. To avoid doing that, make sure that when creating room templates, you don't use any tilemap layer with colliders (https://ondrejnepozitek.github.io/Edgar-Unity/docs/basics/room-templates#designi...). Also, custom tilemap layers handlers might be useful (https://ondrejnepozitek.github.io/Edgar-Unity/docs/guides/room-template-customiz...).