The roof generator doesn't seem to understand that

Indeed. Is not an AI.
You need a trick. Something like this.
Add a very tinny part at the room (1 cm or even less). You will have to test.

I've zoomed to be more visible.

The roof generator.

Final result.

Good luck!

Thank you @dorin, this worked! I put an indent on that wall just in the room I used to generate the roof (not on the actual wall of the floor below it). Thank you. Just speculating here, would it be possible in the plugin to do reference points in the room or something like @keet said? I am not even sure what a room point is, but maybe that is something to go on for future versions?