They're allowed to pick people up for any trip that doesn't start and end in Toronto. It's not an exception, it's just how the rules are written. Where they do get exceptions is for trips within Toronto. YRT used to have one for trips between York University and Downsview.
Probably because it got too expensive to justify the cost of using the TTC for those routes, but it's still not expensive enough to cut routes like McCowan, Birchmount and Warden.
Public Transit in York Region operates the same way that it did in pre-amalgamation Toronto. Individual municipalities in York Region don't make public transit decisions, and TTC routes still run into Vaughan (165, 35, 107, 105 and 160). The only routes being affected by the subway extension are the 35 and 107 - the other three are still going to run to Downsview, Wilson and York Mills.