The exception to this is the Trail Crest/Exit permit, for some reason the management expects you to come cross Trail Crest the day you said you would...not a day early because you chewed up more miles than you thought you could or a day late because you were sick...or decided to an unplanned side trip.
Yes, technically speaking, Trail Crest is a re-entry point into Inyo National Forest so it is treated almost the same as a second hike (on the same permit). The purpose of the exit quota is to limit the number of people bypassing the main trail entry quota by using other Inyo National Forest entry points to get to Whitney. Since it determines whether or not people get permits, it has to be enforced to prevent manipulation of the permit system (and be fair to the people who are denied permits). It does not apply to overnight hikes that originate on the main trail, since the permits are already subject to the main trail entry quota.