My biggest concern with an in/on bed tank is the potential for a greater temp swing in sunlight and the moisture associated with it. If you park indoors or burn it quickly it won’t be an issue.
If you add a filter I’d use a water absorbing one like a Zinga.
I agree with you and you need to proactively manage how you use an aux tank. Although my 17 5500 and 09 4500 were stored indoors, my 02 3500 never was. I kept them both topped, and when not traveling, I used fuel in primary, filled it from aux tank, and filled only the aux tank with fresh diesel.
We have lots of heat here in SW TX, so when fueling locally, I fill both tanks with spicket all the way in until first click and never any problem with fuel leakage. As an honest broker, last trip out both tanks full, was only about 150 miles. Campsite nice and level. Snowbird next to us wanted to clean and treat there roof, so I offered to move my clean truck to their 2nd site to not get it sprayed on. So I parked at an angle with low side on the driver's side and a couple gallons seeped out the turnover safety valve and the attached breather hose. Outside temps were around 60°F. Anyhoo, in hindsight and for future benefit, I need to transfer some fuel if I this situation again.
So, using inbed aux tanks can be managed. I've been happy with the ones I've had for almost 20 years.
Finally, just for grins, I checked online 2020 Ram 3500 CC 4x4 dually equipped with optional 50 gal tank for just $295. That's probably the best deal anywhere.
Cheers, Ron