You can try. But I find it a lot easier and more consistent to use the die. When using the nuts, my experience has been the threads on the nuts get reshaped as well. If doing the nuts only method, I'd use a third nut. Tighten the inner two on each other so you can use a wrench to hold the rod by the nuts. It is a pain to try to hold the rod by itself.
I have used nuts alone, but it was always a little hinky and grabby and I had to touch things up. The die is a great addition! Did you put it on "more aggressive" side in, so that when it was coming off it was in the correct orientation? I think so, but I have only used dies a few times to know what orientation is right.
Nuts by themselves will work, I just happen to have an old tap and die set. If you look closely at the die, you can see that the cutters taper slightly. The wider part is the least aggressive tapering down to most aggressive. I did initially put the die on most aggressive side first so it would be in the proper cutting orientation as came off of the rod.
