You don't understand, there's no problem with voltage, but with current.
The problem with external PSUs is that you need a power brick strong enough to support both a 65W Processor (thin mITX limit, I think) and a 200W GPU because that's what now fits into ITX length. So, you'd need a 300W power brick, maybe 350W, something that's not readily available. You can get them, but it's hard, so not viable unless you want to manufacture your own. Or you'd need two external bricks, which is more than inconvenient.
The problem with an internal PSU (where you wouldn't need an HD-Plex DCDC) is that you'd either have to run the PSU all the time or turn it on with seperate circuitry (refer to my experiment for the latter issue).
If you were to run it all the time, it would constantly power the GPU, which would up the "standby" power consumption of your PC way over what is allowed in the EU and would maybe even make the system unable to boot in the first place as GPU and Mainboard aren't turned on at the same time.
Nice research you've got there. I wonder if you couldn't do that with some simple switch that is open when one of its inputs are up (OR gate) connected to both power switch wired to always on 5v AND the signal from motherboard. Arduino is kind of overkill, I think, unless there's a major delay between pressing the switch and motherboard first power signal coming up. Maybe would just need to press the power button for a second until motherboard kicks in but it's not a neat solution.
Why are you so stuck on pushing 200W gpu's in such case? 145W GTX 970 is more than enough for 1080p gaming on reasonable details. add 35W cpu to this and you should be able to run it off single brick on 250W HD-Plex.
At this point I'd also be closer to the idea of using standard itx with HD-Plex because I'd rather use more standard parts if possible.