If you are swapping your engine for something other than stock (v8?)Shouldn't there could possibly be a valid reason for a body lift...gains an inch or two of under hood clearance. In that case you might want to do it prior.
As far as body lifts being cheesey...if done right and limited to an inch or two they are okay. When you go higher than that...yea then can start to look a bit cheesey.