The football train does not tell you much given that by design it had two deadhead moves and ran only a few times a year.
The idea that one can run every train through Penn providing RER type service is also bogus, due to demand, differences in power supplies, differences in consists, etc. Also SEPTA is not exactly world class agency setting example in operations.
What can be done and what is probably reasonable to do is to have a few through runs per day between NJT and the New Haven line once Metro-North Penn Access happens. Something along the lines of one train an hour (or every two hours, if you so desire). What that gets you is removing a few extra yard moves through the tunnels, removing the need to store a few set during the day, allows you to test the through-Penn demand, and to generally evaluate whether the whole idea is worth it. Doing this will not unclog the tunnels making space for many more trains or make the yards obsolete, but will provide certain flexibility by reducing the yard moves through the tunnels and avoiding the need for a few extra yard tracks to store trainsets during the day. And NJT and Metro-North have established relationship, so it is not as if we are inventing the wheel here. The state of maintenance of NJT equipment is certainly a concern, but if you through run only one train every hour, for every set that gets overly delayed in NJ, you could probably find another one sitting in the Penn yards during the day anyway, so with proper planning you would be OK on the New Haven segment delays and cancellations.
If that works reasonably OK, several decades from now a similar arrangement can be cooked up between LIRR and Metro-North for some through running between the Hudson Line and the Main Line, but the payoffs there seem more remote at the current time. The RPA's idea that you could through run everything is non-sense, but some limited through running could be OK and open up commuter markets that today do not exist simply because even driving between points on the NJT Northeast corridor and the New Haven Line is impossible to do in reasonable time for a commuter.