Any Way To Prevent Roof Clipping In Open Floor Rooms?

I had to scrap an entire build because of this same exact glitch. It is helpful to try to limit lofts to inside walls.

In your situation, I would make the roof at the top of the picture go away by building a 1x4 ledge up against the far northern wall. For the roof at the right side of the pic, I would adjust the overhang arrow to short.

I hope this helps and hopefully this will get fixed soon.