On SEPTA's railroad, many of the rush hour trains already exceed the length of the station platforms at which they stop. Not all doors can be opened; so the stops are longer. In typical cases, the Willow Grove platform is only four cars long; inbound North Hills, just three. Five-, six-, and seven-car trains are operated on several lines.
A five-car Silverliner V train is about equivalent to a four-car multi-deck train in seating capacity. The latter cars can make more efficent use of existing platforms. Because of more floor space at the doors, they tend to load and unload faster, too.
For the new commuter rail systems in the West, most station platforms used didn't exist before the services started. That fact suggests that economic and service considerations other than platform lengths are what have led to the widespread use of these cars instead of single-level cars.
John Pawson