Does using electronics with poor power factor affect the pulse power capability of a generator rated for a certain KVA?
It is not not just the power factor that is the issue, it is also the distorted waveform causing poor power factor. It the power factor was low without the waveform being distorted, the power would be reduced, but only because the generator would be producing less power with the same current (W = V X A X Pf X SqRt3). If you know the power factor, you can easily calculate how much power the generator can produce without exceeding the maximum current rating. Check to see if the generator has a kVA, current or minimum power factor rating in addition to the power rating. With waveform distortion, some additional heating may be produced with the same current. However that would be no different than loading a transformer with a rectifier. I believe that some derating may be required for that. 

The time that you can safely "overload" the generator depends on the time and amount of additional heating. Only the generator manufacturer can tell you.