Connections between "rogue" rooms work now, in the simple form without any complex routes for corridors. Some room types prefer to have a centered doorway and it also works, but with the assumption that rooms always start from the edge of the room space. Also, there is a need for a new type of space searching routines which understands different room shapes (the current one checks a rectangular area).
Now I can move to the next phase which is generating other stuff in the level beside the important theme rooms. I have not tried it yet, but I think it's going to be interesting. The manual generation process will hopefully make it easier to control the generation, but I have a feeling that I need to change something. The good thing is that I have sanded the parts of the generation to such a perfection that there is hardly anything left to do but connect the dots.
I also realized that I can change the way small "auxiliary" rooms are connected to other parts of the dungeon. There can be different rules to produce complex houses with room types logically connected to each other. Let's say a shop can have a small storeroom and also a bedroom where the shopkeeper is staying. The storeroom can be connected to the bedroom as well so if you sneak into the storeroom you need to go past the sleeping shopkeeper.