So what if all of your preproduction systems have a genuine FTDI chip in them, and many of your millions of deployed production systems have counterfeits that you don't know about? That'll be exciting.

Quality is a matter of defense in depth. You can't rely on your preproduction system running the exact same way as production. You strive for consistency, but ultimately each chip in each computer is a unique physical object made with different silicon crystals, and being identical is impossible. You want a system that's robust against a variety of subtle differences.

FTDI is just doing their small bit to make everything just a little more fragile and unpredictable where their chips are concerned, and as such their products ought to be shunned.

I agree with your premise, but in this case, for a medical device it would also be a Quality Systems failure. Any change in a component is scrutinized and analyzed for impact. You have no idea how many times (as a software dev for medical devices), I've had someone from Manufacturing or Purchasing come to ask me "if we change (trivial part X) to a new vendor, what can go wrong and how can we test it?" as a precursor to executing a Change Plan.

I'm not kidding. Even something as seemingly trivial as changing the type of paint used on an enclosure can trigger weeks or months of analysis depending on what's in that enclosure.