In my opinion, no. We can't even completely understand all of the chemical reactions (the Maillard reaction) involved in making toast at this point.
Sure, we do have a fair bit of nutrition knowledge right now, of course, and not everything natural is good for you, of course. However, current popular "natural food" at this point has been vetted through centuries of sampling and cross breeding. At this point I would consider it "more reliable" than processed MRPs (soylent powder is made of natural ingredients too but has been very heavily processed to get where it is) for that reason alone.
MRPs are okay every now and then, sure. Personally I would bet against using them all the time. Even in the bodybuilding community where whey protein supplements are popular, the consensus seems to be its much better to get your protein from a chicken breast if possible.
Not really. We still really don't know as much about nutrition than we think we do. That is why eating a varied diet is promoted; because we just don't understand what we need as well as we think we do.
