Ok, tested your approach and yes Projection Master does left some imprints and wacky stuff once you use it to offset your 3D brushes sculpts.
Projection Master read the pixols and “drops” the model to a 2.5 canvas but once you pickup it will reproject the original pixols onto the model no matter what.
I would not recommend that approach as it leaves pretty nasty stuff on the tool, while plating with it and offseting the canvas in projection master seriously damage the tool and confuse Zbrush Pixols, you left with a non viable model.
The technique i was talking you about before its only for 2.5D sculpting/painting but with a lil luck this tutorial will serve you well:
http://www.pixologic.com/docs/index.php/Wrap_mode
Cheers!!