Actually the setup in EWR is perfectly usable for such, as is BWI with a little tweak. If those are not usable as such then neither are the rail connections in Frankfurt (requires a people mover ride to get to most terminals) or London Heathrow (requires an endless walk to get to the Heathrow Express/Connect station). would be usable. Then there is Milwaukee and Burbank and such, as well as Harrisburg which are also possible to bring up to usable standard, as is Miami, and Orlando soon, if things fall in place properly. There may be others that I can't think of right at this moment.
For true interline service, you would need to have the trains available "airside" (i.e. within the security cordon) so that passengers and baggage could be easily transferred without having to be reinspected. Even Philadelphia doesn't have that. Of course, to have that for incoming trains, you'd need to have TSA security for barding at all the stations served by the inbound trains. Maybe they'd only need one small platform or part of a platform for the "air trains." But it would be a problem for riders who want to travel to the airport, but not necessarily go "airside." (Airport workers, people meeting passengers, people connecting to airlines that don't have an interline agreement with the rail operator, etc.) Outbound trains would be easier, as you could have a seperate "landside" station for people not conecting from flights, and no TSA is needed for passengers disembarking from trains down the line.
Aside from that, you're probably right, though BWI would need to have a people mover built; I've done that connection and it's a pretty long bus ride in traffic between the Amtrak station and the terminal. Another that you didn't mention was Providence, RI. I've passed by that many times on the way to Boston. I'm not sure if Amtrak stops there or only the MBTA trains. But that's also another one that needs a people mover to connect the train station with the airport terminal.