(1) I think a much higher percentage of BOS-PHL is connecting beyond PHL.
(2) I think there is far less regular business travel on this route. Not that there aren't a lot of business travelers. But there are many organizations with very frequent travel on the Shuttle routes and they thus negotiate specific Shuttle contracts. I am a lawyer and recently traveled with a client on LGA-BOS v/v. My ticket was almost 50% lower due to my corporate contract because we have big offices in all three cities whereas the client never has a use for the Shuttle and thus their organization, a Fortune 100 company, doesn't have a Shuttle contract. I think there are far fewer organizations who would be interested in negotiating a specific BOS-PHL contract.