As far as I can tell, I have fixed the issues you raised NormandC.
I have attached the result. I changed/re-did some things in body003 as I was messing around, but I think I see the same thing I described initially.
I will note, now, that I have certainly had those auto refine options enabled ever since I first installed FreeCAD some few years ago. I am not saying I didn't set them myself, but I have never seen my parts "overlap" like they do without the options. Just an idle observation to give you additional background.
Anyway, this is what I have tried, and what I experienced:
In body003, with sketch035 attached to either of the large flat faces of "pad matching lifter support"
Pad to dimension works as expected if "reversed"
Pad to selected, opposite, face gives an unexpected result. (Example attached)
Pad to first/last gives an error when clicking OK: "SketchBased: Up to face: No faces found in this direction"
By way of experiment, I tried to pocket the sketch. "Through all" looked correct, but other options ended badly.
If you take the time to come back for another look, I hope I haven't done anything else unexpected that makes you miserable.