BAR and Allan: I have used a pay-per-ride Metrocard at either 59/Lexington and 63/Lexington stations in the past to take advantage of what actually is a free stopover provided that one of these two locations is used to re-enter the Subway within 2 hours 16 minutes elapsed time of first entry to the system.
When a Metrocard is used at those two stations following this criteria the turnstile will read "XFER OK" You will have then used your one free transfer on a single $2.75 pay-per-ride fare.
You can test this stopover using a Metrocard with a $2.75 balance taking note to your time of Subway entrance - the system official time can be found at any Metrocard reader in stations - and remembering the two hour 16 minute transfer time limit to use at either of these two Subway stations. I have actually done this in at least one instance to test this option for myself...MACTRAXX
EXPRESS TRAIN TO NEW YORK PENN STATION-NO JAMAICA ON THIS TRAIN-PLEASE STAND CLEAR OF THE CLOSING TRAIN DOORS