Here's an explanation on why :
Maybe you are not understanding how Elite tournaments work. B.A.S.S. collects a very large fee, around $ 60,000 from the Host city to hold their Elite tournaments in that city. The City also puts out around another 60 - 90,000 + in other fees and associated costs. So Philly is putting out somewhere around $ 150 - 200,000 to hold the Elite tournament.
In return, the city gets promoted in a good light , which draws in tourism dollars. Philly, in hosting the tournament is looking to promote the city and their waterfront region.
Having the entire field run to the Upper Chesapeake to fish the 4 days would defeat that purpose as they would not be showing anyone fishing on the Delaware in the Philadelphia region. That is the main reason for putting the Flats off limits.
As far as " crossing " state lines. It can be done, happens a lot in major tournaments. Permits can be issued. The Delaware and Upper Bay share common tidal water because of the Chesapeake and Delaware Canal connecting both bodies of water. The tide flushes in and out of the 15 mile length of the C&D Canal, so any " invasive "species is already in both waters. As long as permits are issued and each competitior has the correct licenses for each state, it can be done.
The tidal Susky which they would be a able to fish if not off limits, is not under the regulation parameters you listed earlier ( neither is Conowingo Reservoir above the dam , it has its own special regulations. )