No, WNPCs don't effect parameters because parameters just go off of the IVs and not the PID. If you feel confident that you know which value(s) are your most common, I would say you can go ahead and try RNGing with that value(s). As you start to RNG, if you find that you are getting the wrong Timer0 a lot, you can always use whatever it is you are RNGing for a parameter search to see if another value is more common. For example, say you are RNGing Kyurem and you keep getting wrong chatot pitches, well you can use the Master Ball, run a parameter search with Kyurem's IVs and see if you are getting the same Timer0 over and over again. If that is the case, you can try a seed with the other Timer0 or stick to the same seed and eventually you will get the right one.