"It is hard for hospitals to keep their ORs clean with small teams. Mostly because they do not always have good cleaning products or procedures available to keep being on top of contaminations and so forth". I do not believe this is a valid argument to protect small firms.
> Not all manufacturers write their own software and often contract it out
Two words: liability chain. This is standard practice in almost every other industry.
I agree with the rest of your points, but I do not think that IP protections should trump regulatory requirements: if a company cannot comply with certain requirements due to contracts with their suppliers, the device should not be allowed on the market.