Seems an odd thing to do indeed. I think these Toyota EFI systems have proven themselves to be pretty flawless. Maybe for the 'tunability' of a mechanical pump?
I wouldn't personally install an EFI diesel into an old fully mechanical vehicle, but then I'd be looking for a mechanically controlled engine to go in that (as I did with my 3B to 15B-T swap). Each to their own though.
I think I'm going to pass on the FTE and FT and keep searching for a 12HT. I believe it will be a simpler swap for the H motor and simple is good here in Costa Rica. Besides, I like the in-line injection pump, gear driven camshaft, simple valve adjustment (no shims required). Also, it is more in line with lineage of a 1980 Troopy.
When I was looking into it, I wanted an engine platform that had a long run for parts availability, I asked Dave at 4x4japan about it. He said the FTE was the most supported, and has the most readily available parts out of any of the H or HD series engines. I believe they also had a pretty long production run compared to others.
A 12H-T would be nice but they are a very rare engine, all very old now and most likely in need of a rebuild, expensive to buy and the spare parts are like collector's items. The 1HD-T is still in production with none of these issues, and is a generation ahead of the 12H-T whilst still being fully mechanical. If you would consider a 4 cylinder, the later and larger direct-injection B engines are good candidates for a swap. The 14B (3.7 litre 8 valve) is still in production AFAIK, and they are a common engine globally (not in the US of course) in Dynas and Coasters. They are rare in factory turbo form but a good candidate for turbocharging, and there are turbo manifolds available on eBay. The 15B-F (4.1 litre 16 valve) was in production until quite recently and is a more powerful platform. The factory turbo 15B-FT is a rare engine now, but there are some out there with inline pumps if that's your thing.
I highly recommend the FTE, I have a hdj80 with a ft and a manual, a good friend has a FTE swapped 80 with a a750 automatic, the FTE is more responsive and the low first gear in the a750 is amazing off road, Yes the wiring and computer add some complexity but has proven extremely reliable, the Australian’s have proven the tune ability of the FTE to make clean reliable power. The FTE swap into the 80 chassis is really popular and there are a lot of resources out there.. good luck with what ever you decide..