Add me to the confused list. Is the exit quota only for trips originating in Yosemite NP? What's to stop people from walking into the Mono forest service office, picking up an entry permit for Tioga lake (exit somewhere south of Donohue), and then jumping on YARTS to the TM visitor center to begin their hike?
If riding YARTS into the park doesn't work, then why not pay the walk-in fee to Yosemite @ the Tioga pass gate, cut across Dana meadows - following Dana creek - and then contour around the shoulder of Mammoth peak to access the JMT/PCT? If you did take the YARTS bus to TM and ran into a ranger on the trail, how would they know you didn't hike from Dana meadows?
Perhaps YNP is assuming people aren't clever or adaptable and will just deal with the inter-park restrictions. As Schmaltz noted above, NAP/Cottonwood are popular because they're basically 100% slam-dunk, gonna get permit situations, whether for Whitney or the JMT/PCT. In fact, cutting through Miter basin is a double-plus win, because you can cruise down Crabtree to catch the JMT/PCT junction (thereby avoiding the yucky Siberian/Rock creek/Guyot sand slog), and decide to either head up to Whitney & back, or just hike north to wherever you feel like going.
Given restrictions at major points of entry, knowledgeable people will simply keep moving out to the next available THs. Oh, and get off my lawn!