I have a Soda @ 120mm and a Bfe @140mm.
They handle differently, but that's sort of the point. The Soda runs a 70mm stem and narrowish bars and handles in a nippy "traditonal xc" fashion.
The BFe is slacker, has a shorter stem and wider bars, so is more stable in a straight line, but still can be hauled around fine due to the extra leverage. I can't say I notice any difference at all in the BB height, but then the riding I do on the BFe (steep, gnadgery, techy, often filthy wet) is of a different style to that I keep the Soda for - long days out in the hills)
Where the BB height comparison does come into place, is relative to my full sus bikes. Riding slower, techy/trialsy rocky trails, I ground out on the FS and tag pedals and cranks WAY easier than I do on either the BFe or the Soda.
Practically speaking - 20mm difference axle-crown, = what 5 or 7mm at the BB? Add in more sag on the longer fork, and its going to be maybe 3 or 4 mm difference? You can change more than that using different tyres!