If you use FTDI's VID/PID, you're trying to pass yourself off as an FTDI chip, and it is YOUR FAULT ALONE if an operation that does not cause issues on genuine FTDI hardware does bad things to your own.
These chips may or may not contain stolen IP. They may simply be engineered to mimic the interface of the FTDI chips to be used as replacements. That's perfectly legal. Chip manufacturers often make work-alikes of other manufacturer's designs, from individual transistors up to full CPUs. Think of the non-Intel x86 CPUs, made to work with the x86 interface and instruction set but containing no stolen x86 IP. Or hell, think of the whole automotive after-market industry. If auto companies could legally prevent third parties from making replacement parts, you bet your life they would.
Nope. It's fine (but dickish) to detect the other guy's product and refuse to work with it. It's a regrettable accident if a legitimate operation on your own device permanently alters a third-party replacement, but I'd consider that to be the fault of a crappy replacement part. It's not at all acceptable to go looking for such an exploit with the intent of rendering the competitor's device unusable. Intent matters, and FTDI performed an obviously malicious action which has no use other than to deliberately break a competitor's product. Whether the competitor stole the design or manufactured a clean-room work-alike makes no difference. You can take them to court but you can't play vigilante.