Commuter rail is always the most confusing one for me to follow regulatory wise given it straddles both agencies the FRA and FTA. It's governed by the FRA as far as train operations and safety but the FTA is also involved in commuter rail in that it is responsible for federal funding for rail projects that fall under the umbrella of "transit" and as a result regulates some of the service standards that commuter rail operators must follow.
Fact of the matter is that the second pair of tunnels across the Hudson are primarily needed to fulfill the needs of Commuter Rail (NJTransit). As far as Amtrak by itself goes they do not really need any more tunnels under the Hudson. So in that sense the new tunnels are really a Commuter Rail project. I know this blows the mind of many in the rail advocacy community who are very Amtrak-centric on many occasions.
Another oddity people seem to unaware of is that the traffic management in Penn Station as handled by the Penn Station Control Center, is carried out jointly by Amtrak and LIRR, so even though Amtrak owns the station, its operation is not exclusively Amtrak's! LIRR (NYState) actually purchased the right with real money before Amtrak was formed!
So yes, Commuter Rail and Main Line Rail intermingle in many odd ways as is to be expected. Afterall it is to some extent a separation of convenience in accounts management and such, but they share a lot of facilities.
OTOH, generally Commuter Rail and Heavy Rail do not share facilities specially after PATH was disconnected from main line operationally. Oddly, Light Rail and main line (freight) do share facilities usually using temporal separation, but it is uncommon for Light Rail and Heavy Rail to share facilities.
In Europe, there are the so called Tram-Trains that run both as Light Rail and Commuter Rail. I rode one in Mulhous, the line that runs on streets in the city center and then hops onto the SNCF main suburban line to proceed to Kruth and Thann. On the streets it runs on DC power, and on the suburban line it runs using 25kV AC. Quite an interesting operation.