Well, to my knowledge, there is no screw-on fitting to fill an AS fresh water tank. It would normally have what you describe as a "port above the wheel well" to use for filling. I suppose that is due to fear of over-filling and possibly damaging the tank.
I would expect to see a vent for the tank, and normally as far as I have seen, those vents go to the roof.
Perhaps someone else will shed a clearer light on your situation, but it looks like you have most of the logical connections. Have a closer look at the "mystery" connection though, it may connect to a pipe to the roof...
Remember that for "city" water, there is another connection that does not go to the fresh water tank. On my trailer, it's at the rear street side, and is a common garden hose fitting.
If it's to be, it's up to me.