I expect virtually all native speakers to be able to make a distinction in production: you can say NPR, or say MPR, and that's easy and only depends on whether you raise the tip of your tongue or not.

What I don't know is how many native speakers are able to make a difference in perception: can they distinguish NPR from MPR when they hear them? And how easily?

I think they should be able to distinguish them in some way, in some circumstances, otherwise the difference in production would be completely useless and wouldn't make sense. How would children be able to pick up a distinction they can't hear? 

So I expect native speakers to distinguish them in perception, but only in very few cases (very slow careful speech, or watching the movements of the mouth, etc.). In everyday situations I don't expect native speakers to distinguish them at all though, and I don't expect them to care either... Although this NPR vs MPR issue in everyday situations might lead to confusing one radio station with another.