The only thing that seems missing to me is a logical reason to change from Z zero at bottom to the top.
FYI: Your design software and your CNC machine are not capable of making a math mistake. The only reasons that a user would experience different results from "zero to top" or "zero to bottom" would be an inaccuracy in measuring the material or physical placement. In the long run, zero to bottom returns more accurate and consistent results. This does of course, require loosing all the bad habits that zero to top will allow you to get away with.
In most cases those that zero to top have issues with cut thru depth, those that zero to bottom have VCarve or model depth issues. They are usually both solved by accurate material measurement.
CNC Technology & Training
The Ultimate Woodworking Machine
GCnC411 (at) gmail.com