Does it make any difference as far as when the Pkunk arrive in Yehat territory? If the revolution hasn't been kicked off yet, do you the Pkunk just get exterminated or what? What are the effects on the two races relative to whether the rebellion starts before or after the Pkunk arrive, or is the outcome the same regardless?

Playing through it now, and as it happens, if the Pkunk arrive before the civil war, they get slaughtered, and their civilization at their homeworld gets destroyed. If the Shofixti aren't restored by the time said slaughtering is imminent, you can trick them into going back home (temporarily, I'm guessing).

As long as the Shofixti are revived and the rebellion begins, it doesn't matter when the Pkunk arrive.

I have played a game where the Pkunk sphere of influence disappeared before I managed to spark the Yehat rebellion. I still got the reinforcement event when attacking Sa-Matra. This is playing the Ur-Quan Masters, however, I can't vouch for it to be the same with the true original version.