Hank,
My unit is a 2019 2552. I have the hardwired (installed) EMS system as well. My generator output does NOT read on the EMS panel. That means that the hardwired EMS is installed between the receptacle where you hook up your outside power cable and the transfer switch where the generator output connects.
The owners manual for the EMS unit states that it can be installed (wired) either before the transfer switch (where it only monitors outside power) or after the transfer switch (where it would monitor both outside power and generator power). Apparently Phoenix elected to install it before the transfer switch. Not a "senior moment", but I don't think you actually saw the generator output on your EMS earlier.
Regarding the USB cable. The Ford chassis did not have any USB outlets as OEM equipment. In my unit (same year as yours), Phoenix installed a single USB connector on a short length of wire which can extend from the dash to charge phones, etc. I guess they felt they should provide at least one since Ford let the E Series chassis slip behind the times technology-wise. My 2019 E450, while a very capable RV chassis, is about 2005-era when it comes to technology.
Mike