And that's the key. ZFV-XXX fares are PHL-XXX fares. So the valid comparison for ZFV-XXX fares is not the fare filed for EWR-XXX but rather PHL-XXX.

The fare rules for the cheapest F fare, LAA2AKFN ($449.30ow) for the ZFV-LAX city pair read:

Notice the routing rules are actually published as PHL to LAX. Additionally, the fare rule itself permits both PHL-IAH-LAX and ZFV-EWR-LAX. So when you search ZFV-LAX, you're pulling the PHL-LAX fare (which they've set to be competitive with the AA F fare), not the EWR-LAX fare. That's not malicious intent on UA's part, it's just how the airlines' systems are set up. It also makes sense, because on the ZFV-LAX route, UA is competing with AA, not with its own flights out of EWR (a different market).

Complaining that UA is charging a big premium for the ZFV-EWR segment is no different than complaining that PHL-IAH-LAX is more expensive than EWR-LAX. There is no concept in the airline pricing systems that UA is charging some massive premium for the ZFV-EWR segment; the fact that ZFV-EWR-XXX fares traverse EWR as a connection point have absolutely zero to do with the O&D fares UA files out of EWR. If you want the cheaper EWR fare, then you have to start your journey in EWR.

Fortunately, that is easy enough to do in this particular market because it's pretty cheap and easy to buy your own Amtrak ticket from PHL to EWR or even just to get in the car and drive the hour and a half yourself.

Now, complaining that there's such a huge difference in price for two airports close together is a valid complaint (although usually it's the other way around--people who work/fly out of EWR complain that fares at PHL are much lower than at EWR--hence the existence of this thread, which is filled with people asking how to cheat the system and take advantage of the lower ZFV fares without actually having to travel all the way to ZFV), but that's a separate issue involving market pricing elasticity issues and has nothing to do with the fact that an Amtrak codeshare segment between the two markets exists.

It'd be no different than me complaining that AA charged significantly higher fares to fly out of MDT (20 minutes from my old house) than PHL (1.5 hours away), even though most AA flights out of MDT routed me through PHL, so they were effectively charging hundreds of dollars for that short, 20-minute flight. The answer is that it's a different market and is priced independently from the PHL market; the actual MDT-PHL segment was immaterial. If I wanted the cheaper fare out of PHL, I had to get myself from Lancaster to Philly (which I always did, as I'm a price-sensitive flyer).