I think the feeling was that no trains will be going through Paoli without stopping so there's nothing to be gained by providing a through track ("back in the day" there were a lot of freight movements through there, but that's all going via Reading now and for the foreseeable future), and a third passenger track would require another platform, with all necessary stairways, escalators, and elevators. The PRR handled Paoli locals, through trains to and from the west, and freights with 2 platforms plus 2 through tracks, and not even the Broadway skipped Paoli*. So the new arrangement has the same number of platform faces as the old one with the advantage of being one island platform instead of two side platforms with four tracks in between. As for the two center tracks ending short of the platform, all trains will be slowing down for the station stop anyway. In the case of a local and an express arriving simultaneously, that can be handled through scheduling -- and on-time performance, but that's a whole 'nother subject.
* In fact, from about 1935 to 1938 everything going west of Paoli changed engines there from electric to steam and vice versa -- that must have been something to see.