By the time the Relief Line is built, PRESTO should be in place, which means that you do not need a fare zone, the PATH itself will work just fine for this purpose.
If we do have a NPS station, with PRESTO you should be able to leave NPS station fare zone to the PATH and then enter Osgoode/Queen station with the tap of the PRESTO card and not be charged.
Therefore, the main concern as I see it, is if the added transfer time would add enough to the total commute time to make transferring at Pape not as desirable as with an interchange station at Queen.