I'm not saying that what FTDI did was completely right... but there would have been absolutely no problem for anybody if the "fake" chip designer had simply advertised and sold their own WunHungLo USB-UART Bridge which is completely compatible with the FT232RL, labelled and sold under their own brand.
If you advertise your own Brand X product, and make it completely compatible with the FT232RL, nobody will have a problem with it. FTDI won't have a problem with it, and if you offer the same functionality at a cheaper price I'm sure lots of customers will buy it.
It's the same as the "fake" Arduino boards, to name another common example of a Chinese cottage industry. If you say we are Brand X, we're selling Brand X AVR dev boards, completely Arduino Uno compatible, but ours are half the price, then lots of people will still happily buy them. They're not "fake" or "counterfeit", the product is still exactly the same product at the same price, without the controversy.
But they don't do that - they have to be dishonest about it, and label/market the chip as being an actual FTDI FT232RL, or whatever, and that's where people understandably start getting annoyed.
The test writes to EEPROM on non-genuine chips which would eventually wear them out and really brick them.
But surely you only have to run the test (testing an EEPROM write, the same way the FTDI driver code does it) once. You don't need to run it thousands and thousands of times and wear out the EEPROM.