Putting the arms on doesn't affect ground clearance at all ... the inner hole on the wishbone is still the inner hole, middle hole is where the outer would have been and the new outer is for use with a touring car shell
The later UM521 arms only have the original 2 mounting holes.
I run my cars with the original tower, original length shock bodies and 54mm shock shafts (these are the key really ... wide or narrow rear end!)
All that said I am looking at goging to the shorter shock bodies (still on the Atomic Carbon tower as I prefer the car with the shocks less inclinded than is possible on the plastic towers) for the summer as I like the idea of the lower tower height as it will be less prone to breakage (that said I've run an RB5 since 2007 and as yet only broken one rear tower .. car faired a lot better than the B4 that hit it!!!!)