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".