The bottom cut is done first in order to eliminate the effects of the foam lost due to the cut (kerf). The compensation that CompuFoil automatically handles is the undercut at the leading edge due to the cut transitioning from a horizontal cut (compensated for by the foam dropping down), to a vertical cut (not compensated for by the foam dropping down). Once the bottom cut is finished the top section drops down and the top surface is then cut to the true profile surface.
The cutting from leading to trailing edge is to maintain a good trailing edge cut. This is primarily most important for the second cut as the wire can easily drag the feathered trailing edge with it and roll it over. You could cut the bottom from trailing edge to l.e., but you would have to redo you F/C system for the next cut.
Although it wouldn’t have been a problem to code CompuFoil to allow for the kerf so you could cut the top first, you then end up with the bottom bed too deep and would be much more difficult to use for the vacuum bagging process. So it’s not really a matter of not wanting to deal with the kerf, it’s more for practical reasons that I don’t do it.
If you really want to do the top cut first, CompuFoil will accept negative sheeting thickness so you can in effect compensate for kerf.
Hope this clears things up!