Right now it seems that ProtoMechs are only used for Trueborn Aerospace pilots. Could ProtoMechs be retooled for use my Trueborn Mechwarriors or Elementals? What about Freeborn (Clan) pilots? What about Inner Sphere people?
The answer is...it depends.
The reason why the pilot phenotype is used is simple.
No others would fit.
The typical Clan pilot is 4, 4.5 feet high - the size of a child. They are small and ProtoMechs are too cramped for a normal cockpit, with engine and weapons, etc. You could probably build something similar to Protos fir larger but it wouldn't be combat viable.
So, the answer to your question is no other phenotype would be used because no other phenotype could be used.
As for the IS...that has been looked into. The possibility of using children was considered and dismissed. The WoB used Quadruple amputees in its protomech program but by and large, Protos aren't a good fit for the IS. Maybe if they'd been more popular but between rules and looks, they never took off and have been relegated mostly to flavour units for the Horses and Ravens.
The elephant in the room is that CGL appears to be making a quiet retcon to increase the size of Clan pilots. There are one or two stories where they seem to no longer unnaturally small...simply freakishly thin. This change would explain why Randall Bills wrote a story whereby a Mechwarrior phenotype was able to enter a ProtoMech cockpit and find himself merely cramped, whereas previously he would have had trouble fitting anything other than his head and torso....witness previous canon on the necessity of using children and quadruple amputees, never mind the entire reason of using the pilot phenotype in the first place.