We charge the same for 3 color spot and 4 color process. 4 or more spot colors costs more.
We have in house high end separations capability which allows us to make spot or process film at a very affordable cost. Given that, our experience is that the major differences are as follows ...
1.) spot colors require ink mixing, process does not. Inks are mixed by weight with most colors taking 15 - 20 minutes to obtain a formula, weight out and mix. If you're doing 4 or more spot colors, thats a fair amount of extra time for the job.
2.) spot colors require you to completely clean the machine after each run. This can take a fair amount of time as well. If you run process ... and do process job after process job all you have to do is swap screens re-ink and off you go. So spot colors add to down time between jobs which translates to increased cost.
In short ... spot colors require more labor which has to be factored into the cost. In the cases where its appropriate to get the best results then the improvement in quality is easy justification for the cost difference.