For what its worth, the DL-212As (ex-L&N) that I am familiar with have one aftercooler on the engineer's side, up high and just ahead of the radiator shutters. This is piped in between the compressor and the main reservoirs. An intercooler (on a compressor) is another animal, a set of tubes and fins located between the LP and HP cylinders.
Some educated speculation on the use of two large aftercoolers on the FPA-4s: In Virgil Staff's "D-Day on the Western Pacific", there is a long discussion on train lines freezing up in cold weather on the FTs, F-3s, and F-7s. This was in the mid-50s, I believe.
Westinghouse Air Brake did a lot of research, using units instrumented with thermouples, and found out that in some cases the last bit of cooling took place in the train line. The air was too moist going into the main reservoirs, and subsequently froze up in the train line.
One of the solutions was more radiating area ahead of the reserviors, as well as some form of water seperator/trap. (Today's spiral shaped Salem units come to mind here, perhaps an earlier version.) I recall reading that the added cooling was more effective than the traps
I suspect that the designers at MLW had access to this information when they laid out the FPA-4, with two large coolers. And it being potentially colder up in Canada than down here, it was apparently the right move. I've seen videos of some of the VIA trains in some really extreme weather conditions; I'm sure all that extra aftercooling helped.