You most definitely cannot fill diesel in your second tank as it is connected to your generator tank. Once your generator tank is exhausted of fuel, it will automatically drawn from your fuel station.
I think RVIA regulations limits the size of fuel tanks, so to skirt this, they have installed two tanks. Essentially killing two birds with one stone by combining a fuel station.
My truck is a diesel as well and I pondered the same question you have as my f250 has a 26 gallon tank.
I plan on installing a 50 gallon Titan tank which replaces the oem tank. Best thing is my "miles to empty" can be recalibrate at the ford dealership to reflect the new capacities.
I'll have the ability to tow 500 miles at a time with the new tank.