Looks like you have to draw a room by hand. I can't see the far side on the card board model but I think it's a long straight line. Anyway, draw a room as if you are looking at the top of the roof from above. Make the room a little bigger than the outline of the hexagons for overhangs. Make sure to add extra room points at each side where the top of the roof is. It's probably easier if you first rotate all walls so you have horizontal lines to work with. Use that room with the roof generator. (To rotate install the Plugin Manager and use that to install the advanced edit plugin which adds a rotate function for everything selected and some other very useful tools.)
If you can't get it to work upload your .sh3d project file to a host and post the link here. Then I can see what what I can do. Make sure you have something on it that comes close to the roof you want, even if made with multiple objects. This is to have a view from all sides.
Most of my projects involve dodecagons (12-sides instead of 6) so I have some experience with strange corners
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