The V7 holder is intended to be printed with supports to have the smooth topside for the hands-side.
So if you simply print them in T-orientaion its perfectly fitting the build plate.
On the two gears-Shafts:
I never had an issue. First layer height =400um, then all fits, it also helps adhesion.
Some slicing programs also allow to place at negative z.
Another comment/make shows another way of fixing it.