Just jump on board with GP and digging in (good stuff!!).
For our CPT client pages we are stripping it down to just was is absolutely needed and I have removed all the standard right hand side meta boxes (like Featured Image). However the “Sidebar Layout” and “Footer Widgets” boxes are displayed with GP.
I don’t mind working in the code (hence my like of GP) but this would be a good enhance to have the chechbox option to not display meta boxes when creating a CPT like other areas (assuming that is possible).