I've used both set ups at work, and my 97 kinda has all 3 mentioned
. The oversized factory replacement is nice because it doesn't take up bed space, but ya, they have gotten expensive.
I have a 100g transfer tank in my truck and they're sweet because you can fill other trucks, equipment, fuel cans, ect. I don't have it plumbed into my factory fuel system, but I could easily off the 1/4" npt drain.
On the other hand, it's kinda large and will be a pain if I want to put a cab over or whatever in. A thin tank that went right up against the cab would be perfect for me. But I can see how you want to utilize the space under the tool box.