Sounds like you're on top of things, Kevin, in particular with not closing the overflow hose when filling. I regularly dump all of my tanks and travel completely dry, filling only when in-or-near camp, so a lot of time doing water management.
Tanks are weird. And filling tanks can be weird, too, for all kinds of surprising reasons (less surprising with some fluid dynamics, but surprising nonetheless).
I think listed tankage is generally pretty accurate, as the tanks (and water heaters) purchased by Rockwood have known/measured capacities that can be published. Rockwood specs and buys a 50 fresh gal tank? Rockwood puts 50gal on the freshwater capacity. Rockwood specs and buys a 6gal hot water heater? Rockwood puts 6gal on the water heater. Completely fill that empty tank AND fill the HWH? You've got near abouts 56gal aboard. I did the
drain-and-measured-fill thing and got pretty close to listed tankage, especially for the known qty of the fresh tank (black tank is more of an estimate, though, based on the appearance of water near the bottom of the toilet side pipe, which extends INTO the black tank - so I don't think the listed measurement is wrong, just that my experiment wasn't accurate).
However, since the (below-floor/in-frame) tanks are predominantly flat and book-shaped, ANY off-axis FILLING or DRAINING won't have the desired effect (to fill or empty to completion), and this tilt can have a LOT of impact (and, in particular, on book-shaped tanks). We all know the idiot lights aren't accurate. When you see the sensor placement in the side of a tank, you'll see the reason why...
View attachment 1107718
Here you can see the fill port (top/center) the vent port (top center, next to fill), the sensor array (to the left), the water draw point (bottom/center) and the dump (very bottom)
See the very top sensor? The one that - when it senses water - lights up the idiot light that reads "full?" This tank still has some more tank left above that. In my case, it's 12 gallons worth of difference btween the light coming on, and the tank being REALLY completely full (to the point of water coming out the vent port). And if you take a tank that reads full, with the light JUST coming on (and the water JUST up to the level of the sensor, but not all the way away from it), and then tilt the tank away from the sensors, the full light will go off.
The vent port should be at the same height as the fill port - and in this case, it is. There's is likely a little bit more room in that tank, but it seems to be a negligible amount. still, across the entire surface of the tank, that could add up to a decent amount of water.
Likewise, the external vent height GENERALLY should be at the same height as the fill entry point (note how this is different than the ports in the tank, this is actually where you interface with the tank - fill entry point on thd side of your coach or in your wet bay, and the vent hose or vent port). If the vent is any lower than the fill, then water put into the tank via the fill port will overflow out the vent before backing up the fill port. Nowadays, many RV fresh tank vents are co-located with the filler hose inlet... however, some aren't and if your overflow hose is at a lower height than the fill spout (or air vent), then you'll get water out of that before water comes out the filler inlet.
Tank dumps are impacted, too - but can mostly get around this by virtue of (1) a low spot can be manufactured into the tank with a drain attachment there - as shown the above - or (2) tank bulging, with a drain attachment in the low spot/center of the tank (though this placement creates a(n acceptable) weakspot in the tank floor). But if your Arctic Wolf was tilted away from the drain port to any degree when you dumped last year, your tank could have still had water in it.
And, as others have mentioned, if your vent hose OR filler hose gets a kink in either of them - of are blocked by any manner, it can cause problems with filling your tank, even to the point of pressurizing them, causing them to change dimension/swell like a ballon - an issue that can cause floors to pop up, or tanks to drop out.
Lastly, if your flowmeter is even remotely out of calibration, it will (most likely) underreport how much it's filling.
But you know all of this.
I'd be tempted to (1) super duper level your trailer, (2) dump everything, (3) calibrate your flowmeter by pumping a known/measured quantity of water (like pulling water out of a 5 gal bucket), and then trying again.
Sorry for the length, hope this helps. I could be - and often am - wrong.