It's been ages since I've dealt with anything custom on the Pyra, I've been spoiled with pre-built images that just boot when inserted. So I don't believe there is a magic key, it just needs to be bootable. I remember the makeSD script being a bit half baked as well.
I need to research it myself on how you set it up with the make tools, but you could compile statically, in theory it will bring in all the dependencies into the binary, it will make a larger binary, but in theory OS independent.
Just something to note if it's not understood by everyone, the blue USB port is not USB 3.0, it's ironically USB 2.0 only with SATA lines where the USB 3.0 data lines would be, there is a breakout adapter that will give you a SATA port for sale on HNS page. I've observed USB 3.0 devices getting...