Joe I think you're thinking about it all wrong, it'll print the support on separate layers than the main part no problem, I've done it on numerous occasions with S3D and custom designed support. It works great to print support at 1/2 layer of separation, prints come off the support beautifully and the parts look great! ABS doesn't peel up from support either.
Z height changes are not an issue, it'll just change z-height twice as many times, each time you retract, you change z height if you have z lift.
Here is a part I designed support for, I used .25mm layer heights, .5mm nozzle, offset the support from the model by .125mm, created separate processes, it printed beautifully and the support actually worked - unlike S3D generated support - the part would curl off the support in certain areas. Print time was about 1/2 hour shorter than S3D generated support!
