You have a better grip on this than I do, so help me understand where individual engine fuel flow is on this chart:
I think there is something you misunderstand. There is only 1 PGN for fuel flow.
But each PGN can have a number of instances. So the Merc Gateway occupies X number of instances where X = number of engines/tanks etc.
So Engine One will be instance 0 / Engine Two will be Instance 1 (examples only)
I have 4 active GPS receivers - sharing the same GPS PGNs.
Mercury Axius GPS = 0
Garmin 19x = 4
Simrad NSS8 = 5
Lowrance HDS Touch =6
All the above transmits using the same PGN - but my N2k network can tell them apart because of their individual instance numbers.
I have manually "set" the instances on all but the Mercury stuff (Setting instance number is one of the bugs I have reported. Setting instance number is a USER applied field - not an auto-set field for the device to fill in itself.)
Most times you wont have to use instances. But once you have a lot of things

on the N2k bus of the same type - that is when you need instances. In most cases you wont even notice an "instance problem". But .. again - Raymarine as far as I remember - is the ONLY MFD that cant set Instance numbers.... Ergo - it can't ever get NMEA 2000 certified.
If you look at the PGN numbers - the Fuel flow shares its PGN number with a lot of the other "sentences" (Oil, Fuel Pressure etc etc).
The only reason for not seeing the PGN for both engine instances - is if the installer (Sea Ray) forgot to code your engines SmartCraft system as engine 0 and engine 1. That has been seen quite often especially in the earlier SmartCraft installations.