That is a good point.
I have never noticed as I always tend to have some overhang.
Setting a temporary offset in the info box or roof settings dialogue works as you mentioned.
Setting that back to zero afterwards works for me (don't use 'undo').
When editing the edges manually remember you can also offset all edges at once in the pet palette.
However the solution to your problems is to select the roof then so long as you have the roof tool active you can just draw the hole that you want over the roof (the same works for slabs and fills so long as you have the correct tool active).
No need to use the pet palette at all to cut a hole.
Barry.
One of the forum moderators.
Versions 6.5 to 27
i7-10700 @ 2.9Ghz, 32GB ram, GeForce RTX 2060 (6GB), Windows 10
Lenovo Thinkpad - i7-1270P 2.20 GHz, 32GB RAM, Nvidia T550, Windows 11