I've encountered this issue for some time and honestly the trouble has been so minimal it's hardly worth mentioning, but I figured I'd put it out there in the spirit of learning something new just in case I'm doing something wrong.
Final Product for reference ... The mold/details shown below are only for one half of the casting mold ...
The pedestal is already present from a cavity cut in an assembly ... Just trying to remove the excess material ...
End result I'm looking for ...
Basic extruded cut trying to remove the excess material ...
Results from the cut ...
Results from the cut with the draft reversed ...
So, I guess where I'm going with this is that it's just odd that the draft has to appear to be backwards for it to work properly. "Flip side to cut" has been checked and that likely plays a role in reversing everything, but it never fails that 99 out of 100 times I initially do it wrong. This part is very basic so I thought it would make a good example. Our typical parts have a level of detail that makes doing the cuts from other surfaces difficult if not impossible.
John,
If you are trying to make 1 the negative of the other it might just be easier to make the 2nd half as a big block first and then just line up the first piece and use a Combine Subtract. This way you will get a perfect negative and don't have to worry about messing with the draft on the other part.
As far as to why the draft is the incorrect direction 99 out of 100 times, I'd say it's like the toast always landing buttered side down . Kinda same thing I always feel when doing any feature in SolidWorks is it default picks the direction I don't want.
~Eric