Can I add a layer of complication in here?
NYC-PHL is a very short sector, and iirc, CO now code share with Amtrak. EWR has its own station, but in their infinite wisdowm, Amtrak's fasters Acela trains don't stop there.
However, if you had a LHR-EWR-ZFV routing, where 30th St station was the final destination, you may be priced for the 'inconvenience' of an indirect routing, whilst the flight itself is still direct. If you actually wanted NYC, could you then bin the ral sector - after all, booking systems are completely different, and they don't take your luggage.
Just a thought, not something I'v ever really got behind the small print on.