Something similar to the pink validators would definitely be needed for LIRR at Jamaica, Floral Park, Mineola, Valley Stream, Lynbrook, Hicksville, and Babylon, as those are transfer stations that may bypass more expensive zones.
For the subway, out of system transfers would be handled by the OMNY fare engine since there are no fare zones (assuming no change in transfers and procedures), so no need for that.
AMEX should issue you a new credit card if you mark the current one as damaged.
I'd imagine that the fare engine wouldnt provide for a free transfer, just like how airtrain is set up today.