I don't think you understand premarketing approval (PMA). Companies don't "run clinical trials and then submit for approval". The order is reversed.
Companies submit a PMA application first that details everything about the process upfront, after spending a significant amount of time going back and forth with FDA scientists and advisors. Once the FDA officially accepts the PMA application, then and only then can clinical trials begin.
Modifications to the PMA application after it's accepted have to be negotiated with the FDA and inevitably lead to delays. Changes to the manufacturing and quality control parts of the application are actually some of the easiest to make as companies frequently make improvements, but the "minimum viable product" for the PMA application is a very high bar to clear. They have to be able to prove that they can manufacture the drug reliably long before they give them to patients.
Many years later, when phase III results come in they are evaluated against the success criteria in the (at this point many years old) PMA application. If the drugs works, the FDA approves the PMA application, giving the applicant the right to market the product only as detailed in the application.
> I also did point out that the integral nature of the manufacturing process is a obvious potential problem. It, however, does not seem like a insurmountable problem.
The problem isn't manufacturing - that's really the easiest part of the whole process. It's the intellectual property and the nature of the medical approval process. It's an upfront all-or-nothing investment of tens of millions of dollars, minimum.
There are no shortcuts and without the rights to the patent, it is for all intents and purposes insurmountable. When a company does have rights to the patent, though, it's no longer really "third party."
I also did point out that the integral nature of the manufacturing process is a obvious potential problem. It, however, does not seem like a insurmountable problem. The specifications on sourced components and the quality control processes applied to them is already integral to the drug manufacturing process. This would just move it one level further up where the final drug produced by some existing production process is a “component”. They also already approve drugs for different uses and evaluate existing drugs for new uses, so it does not seem that qualitatively different from some existing approval procedures. I am not sure of the exact details and am not proposing a specific solution, but it certainly does not seem to be a deal breaker.