Let people wait on the platform as the train arrives. This is something that basically every train operator but Amtrak does.
> The tracks do not support all operators and the station design divides Amtrak from LIRR
This isn't a problem... trains in most stations are already basically scheduled to an individual platform anyways.
> Trains are terminating at NYP which requires a longer process of ensuring no passengers are still on on board before leaving for the yard.
Through-run trains. Yes, this requires cracking some heads at NJT and LIRR (and MTA before much longer). Is it really worth spending billions of dollars to avoid having to resolve agency turf fights?