Nick's programmer does not use AVRDUDE. It is run from a serial monitor or terminal program talking to the sketched Arduino. All the fuse and lock bytes are in the sketch as well as the hex 
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What I mean is that after bootloading via Nick programmer, Arduino as ISP and low level AVRDUDE cli for setting fuses don't work. I think it has to do with an AVRDUDE bug and setting the lockbits. Uploading sketches work fine.