DrAzzy:
I think the best course of action is what Pert suggested - nano or pro mini clone without pre-soldered connectors, and solder on round pin header. That gives you a gap of ~0.2" between the boards.You can also solder a pro mini (but not a nano, since there's stuff on the underside) directly onto your circuit board - put holes matching the pro mini footprint on your PCB, and solder it down. Making the connections can be tricky, but it's not that bad. I position the board, put no-clean gel flux on the holes, and then solder them - when the solder finally wets the metal around the hole in the PCB you're soldering it down to, you'll see the solder suddenly appear to get sucked in - that's what you're going for. Also inspect the board from the bottom to make sure you see solder on the underside of all holes. I've used this method in a number of designs, and it's now my favorite way to mount pro mini's on a larger PCB - though I would hesitate to use it where the board will be exposed to significant vibration or flexing.
I think if this (or another) project becomes so definitively "done" (meaning no more PCB revisions likely ever), I might do something like that. In fact most of the China based PCB fab houses I've worked with don't charge any noticeable amount more to cut rectangles or slots into your boards. So I guess I could make a rectangle just slightly smaller than the NANO, so I could place it flush without the USB chip and other bottom components hitting the board, and solder edgewise like you're suggesting.
But this current project is still a little "early" for me to make a permanent attachment. So if I can find some female headers a little lower, without costing 20X more, I'd buy some.