Any Way To Prevent Roof Clipping In Open Floor Rooms?

I have stopped trying to get it to work! Now I use multiple roofs to avoid having the roof actually go into the space.

For your half-hipped roof situation, I would have one half-hipped roof that goes from left to right but is only as deep as the front of the extended room. Then I would have another half-hipped roof rotated 90 degrees that goes from the front to the back and goes all the way to the side of the extension without going through it and then mirror it on the other side.

I copy the roofs so they have the same slope. The roofs overlap well and play nicely with each other so it can be an alternative that allows you to have the same space configuration without the roof going into the house.