Both types of pumps run the liquid fuel through the pump's motor. From ~1/3 tank down they'll run about the same temperature. I can see where the external might be more prone to heat related failure, but I don't read or hear of them failing left and right.
External pumps tend to be noisier than internal pumps, which I suspect is the reason that the OE's have been putting them in the tank. Any external pump mounting method needs to address both broadcast noise and conducted noise. I've been giving this some thought for my FJ project as I plan to use an external pump so that I'm not married to any particular tank. Read: Stock tank for now, but eventually I will want more capacity. If you're interested I can make a quick model of my idea and post a jpg.
FWIW I'd be wanting both tanks, the under-seat and the "CJ".
The Ford pumps tend to grenade occasionally when used externally (from what I read), which require filters before and after the pump to prevent chunks moving downstream. There are a couple pump options that people say are more reliable, and I'll investigate them. Any external fuel pump would require a spare on hand at all times, where I would be less concerned about the internal pumps.
15-20 gallons is about what I'd want for now, but having multiple would definitely make longer drives easier. It's all a question of how it fits into the overall project budget. I can always upgrade/add later.
Would fuel cell be an option? You could put it behind the middle bulkhead. The double tanks under the seats sounds the easiest but sitting on top of all that fuel might make me a little nervous.
I do not want to lose any cab space, since I have 3 kids and a wife to think about. Fuel cells have their own problems in this application, although I did consider them for a while.
Series 88s all have tanks under the seats, as did early Jeeps and countless other vehicles of that era. Part of the attraction for the CJ tank is that is gets the fuel out from under me, freeing up underseat space for storage or perhaps a water tank, on-board shower system, or some other "glamping" accessory. Every inch counts in a short wheelbase vehicle.