I'd think so. If I remember right the so-called protection Tommo did was to re-write the pinouts so a normal reader couldn't do that. This setup seems to come with an adapter that re-tweaks things around so you can toss it into a PC and throw whatever you want at it that sticks, then put the little card back into the NGX and it works. I imagine you'd need some working knowledge how to throw more emulators and ROMs at it other than just Neo Geo stuff though.
I think the NGX itself used normal SD sized cards, so the little micro would be normal, so you'd need a micro to sd adapter and go from there. Then once you put what you want on the little card, stuff it into that chinese custom hacked sd adapter and the NGX will pick it up.