Line 83 of the physics.cfg says the following:
buoyancyRange = 1000 // If altitude of a part is greater than this above sea level, no expensive buoyancy checks are run
KSC ground level is at 69 meters. So this means all craft have these buoyancy checks when landed. I can only imagine this has an effect on large part count vessels. I haven't tested just how much this might affect performance, it's probably not much.
But anyway, I think a better value would be 10 meters.