I should clarify that when builders take exception to boring out a case to
its max its usually for highly modified engines which place a much greater
stresses on the bottom end. For a stock rebuild it may not be a problem at
all. I'm not an expert myself and I'm sure those on the list who are will
clear that up. My information says 0.060" is the maximum oversize you can
safely bore but I don't know if this has changed for the waterboxer

As well, you are right. It would be impossible to align bore without fixing
the case to a stable surface as what the case is affixed to is an essential
part of getting the perpendicular within a fine tolerance and should be an
inseparable part of the rig. This being said, of the two rigs I have seen
powered by drills you would hardly call them portable.