That's not quite what I meant or how I work! What appears to have happened here is that, over the years, the guitar has moved away from its original "compromise" tuning as you mention, possibly due to saddle wear from the description. What I try to do is to restore the instrument to its best "compromise" tuning across all keys, not a pure 5th in one. That's more or less what Frank also aims for on frets.com. Hope that clarifies a little.
I always approach guitar setup (and I do a lot of it) as a "holistic" job with a variety of contributing factors.