A smartcard would presumably also work on Metro-North and LIRR, which
are also the MTA, with the remaining question being NJ Transit.

The question yet to be answered is how to verify a passenger's length
of journey on distance-based fare commuter rail systems.

This is not exactly a new problem, you know.

On regional rapid transit, they do so by having turnstiles at both
entry and exit, so the exit turnstile verifies the ticket is valid
for the distance travelled.

But on various large commuter rail networks there are no turnstiles.
Adding turnstiles would cost a fortune, ...

Which is true, but there's no need to do so.

The Caltrain commuter trains between San Francisco and San Jose let
you pay with the Clipper smart card. All of the stations are ungated, but
there are Clipper readers on the platforms. Before you get on the train,
you tap your card, after you get off, you tap it again.

If you don't tap in, and a conductor checks your ticket, you get
fined. If you don't tap out, you're charged for the longest possible
trip from where you got on, so it's in your own interest to tap out.
Commuters get a monthly pass on their card for the stations where they
get on and off, and the conductor can check the card to see that the
pass is valid for where they are.

This isn't rocket science. Every system I know that has smart cards
and distance sensitive fares does this, from the Seattle light rail to
TfL in London to the Maokong gondola in Taipei. On the London
underground, most of the stations are gated, but some aren't, and you
have to be sure to tap in and out or you risk being fined if there's a
ticket check on the train or the platform.

R's,
John