Yes, you're right, typically isolation results in isolating away or otherwise losing useful fractions such as you mention.
From the standpoint of what the industry can do, assays can determine exactly what any given product from various sources contains. From the standpoint of the end-user, I suppose it would be impossible to determine content of such fractions.
I am really not at all a food science chemist let alone with speciality in current methods of protein purification. It surely would be interesting, but I don't have that depth of information as to what processes have what advantages.
While most likely some processes just flat aren't as good as others, I suspect that it probably is more generally the case that it depends more on the particular producer and the particular product than on being a specific general method, and most likely what may be the method used by something that's up there, but not quite the current best, may be the very method that in the near future yields the very best.
So even if I had more information on methods, it probably would be very time-perishable information anyway. Still it would be interesting.