The Terminus experiment was actually an experiment to see if the PRT/Protectorate system could endure without Cauldron's intervention, since the members knew they were by no means guaranteed to survive the coming Armageddon. This doesn't make the experiment any less stupid or any more valid; indeed, the experiment became invalid the moment they gave Thomas Calvert his powers. Nobody involved in Cauldron's decision making has any understanding at all of proper experimental design or procedure.
Not so much that. The problem is that the Chief Director of the PRT and the entire Triumvirate are part of Cauldron, and if they are denying resources the system is set up to use then it screws up the experiment.
If the Chief Director has to approve transfers or the loan of personnel then it screws with the experiment unless she acts the same as if the experiment did not exist.
If they transfer people out of the Bay but not in, it screws with the experiment.
If they don't send in additional personnel or resources when any other city would expect it, it screws with the experiment.
If they don't allocate more funds to expand the local PRT when any other city would get those funds, they screw with the experiment.
THe problem is that Cauldren members control the top spots in the PRT and Protectorate, so treating Brockton Bay differently screws with the experiment.
As for parahuman fudalism, which is normally what people say the experiment was about, they had plenty of other countries where this very thing happened, so they would learn nothing by letting it happen in a random American city. Why would it be any different for Moorad Nag's country or the CUI?