I'm most definitely not an expert but I do have an opinion/experience on this very question. When I sourced my spare boards, I got a pair for exactly the reason you mention. With such frequent and indeed strange issues concerning the Acela, I decided to hedge my bets over these particular parts.
I have a feeling (based on some research I did six years back) that Lionel might have got in a quantity of the Revision B boards because of the frequent issues over pantograph operation with the original PCBs. Indeed I just looked at my replacement parts receipt (from 2012) and I see that I got two PCBs and two motor and gearbox assemblies. I think that there was some change in the latter as well as the PCB but after this length of time I can't recall what it was.
Anyway I'd go for the extra one. I'm sure Lionel will be grateful for the extra sale.