Not much (if any) will change.
When SEPTA assumed passenger operations and physical plant ownership from Conrail, the ICC and STB grandfathered trackage rights agreements to Conrail to conduct freight operations on SEPTA owned tracks.
After the Conrail takeover, the trackage rights on SEPTA were split up among Conrail, NS, CSX and the 3 shortline operators at the time (West Chester RR, East Penn Railroad, and New Hope & Ivyland RR).
When CSX gave up operations in Lansdale, they effectively sub-leased their trackage rights to Pennsylvania Northeastern, but ended PN's territory of operations at Neshaminy Falls, Tabor Jct, and West Point to assure CSX would be the sole interchange connection with the PN, East Penn, and New Hope & Ivyland. CSX worked out a flat interchange rate with the Surface Transportation Board for the Lansdale cluster. The shorelines charge an agreed upon rate for delivery services.
From what I have researched on the STB website, running trains doesn't cost CSX a penny to operate over their trackage rights on SEPTA's mainline and branch line tracks. CSX is responsible for 5 miles of maintenance costs and grade crossing accident liability on the Stony Creek branch from Elm to West Point. PN is responsible for track maintenance and grade crossing liability from West Point to Lansdale.
Since 3 railroads operate to Lansdale, SEPTA handles the dispatching responsibilities.
The trackage rights for customer deliveries break down like this (according to the STB web site)
Airport: Conrail Shared Assets
Bethlehem Line, Dale to Telford- PN (under sub-lease from CSX)
Bethlehem Line, Telford to Quakertown - ESPN (under sub-lease from CR / CSX)
Chestnut Hill East, Conrail Shared Assets
Chestnut Hill West, Conrail Shared Assets
Fox Chase, Conrail Shared Assets
Ivy Ridge Line, Norfolk Southern
Mainline (Tabor Jct North), PN (under sublease from CSX)
Mainline (Tabor Jct South), Conrail
Neshaminy Line, PN south of Neshaminy, CSX north of Neshaminy
Norristown Line, Norfolk Southern
Warminster Line, PN (under sub lease from CSX)
West Chester Line, Conrail Shared Assets (to Glenn Mills)
West Chester Line, West Chester RR (Glenn Mills to end of track)
***I can't find any STB dockets where New Hope & Ivyland have trackage rights to operate between Johnsville and Warminster to serve Double H plastics.