Whatever weight is actually on the rear axle is what counts toward your rear axle capacity. Doesn't matter how it got there. Tongue weight, junk in the bed, folks in the cab or fuel in the tank. If you go on the scales and get a reading that's how much is on the axle. Adjusting the WDH can vary the weight on the axle.
If you measure rear axle load with WDH connected then that is your rear axle load with WDH connected. Same goes for without. For towing purposes I expect you want to know the load with WDH connected as that's what it will usually be while towing.
If your rear axle load is excessive you can remove some with WDH. However, 500 pounds might be a challenge but I've never tested it.