The Bilevel coaches are an interesting surprise. There are several angles possible there.
1) Bombardier Multilevels (as currently operated by NJT and AMT) have the clearance to operate on any point in the system; early speculation should probably focus here. The MLV is a proven design at this point, despite its NJT Science Experiment origins; MARC just took an order that is technically an option on NJT's most recent contract. SEPTA might be looking to use the remaining 25 unexercised option orders to spin up new car production very quickly.
2) Runs currently operated by the push-pull fleet may be seeing more growth than SEPTA is willing to handle, either with the existing fleet overhauled, or with EMUs. Those express runs have the distinct advantage of being very fast door-to-door, and timed for peak demand timeslots. With platform lengths putting the kibosh on trains longer than 7 cars, the 20% seat capacity boost may be just what the doctor ordered.
2.5) Might SEPTA be expanding the role of the push-pull fleet as peak hour express/surge capacity? If the Reading-side electrical system is getting overhauled as advertised, we could see more push-pull capacity on the Doylestown and West Trenton lines.
3) Has SEPTA found a problem with the bombers that will limit their lifespan, even with overhaul? Maybe the benefit to refurbing the bombers is sufficiently limited that it's more cost-effective to buy new.
4) The NJT option order still represents far fewer seats that currently exist in the p/p fleet. Will SEPTA be leveraging that into a base order of its own? There's really no sense in having more than one type of p/p equipment out there.
5) Maybe the above points are all backwards; instead of a fast startup with NJT's option from Bombardier, maybe SEPTA is looking to slow-walk this contract until after the FRA changes the crash safety standard from buff strength to crash energy management, which is expected in 2015. If true, a multilevel (from Bombardier or another supplier) that was significantly lighter than the current FRA-compatible MLV would be a significant win for SEPTA, and certainly a compelling reason to abort the bomber overhaul program and sell the cars to a startup line on a shoestring budget, or for scrap.