Filling in the gaps in the roofing here?

Oh, that's an interesting picture! And a very complex roofing to replicate. So, I'm not entirely sure, but to replicate that dome, since it's on an upper floor, I'd recommend making a slightly smaller octagon room instead of square (only the dome is higher than the rest, you can see the walls peaking out, and it's a little less wide than the room underneath) and to extend the gabled roof right through that room. It shouldn't clip if the room is closed. A small gabled roof and some chimneys might replicate the part with the rounded window. I did some basic tests, with very little decoration. Here's a look at what I mean, though you'd probably want to pitch the main gabled roof one notch higher than I did, and extend the smaller gable so it doesn't get cut by the main gable. It will poke out a little more than the original since we can't build on the half tile, however :

https://i.imgur.com/fiwzMS7.png