I agree with your post. We as a community have completely subverted the meaning of this quote. It is originally about the need to profile your code, and about how programmers instincts often fail them, making them optimize the wrong things.
But when it mixed with Startup Culture it morphed into "don't worry about speed, just write whatever shitty code comes into your head and only optimize if a customer complains... scratch that, let's not listen to customer complaints because we know better".
Like you said, some companies with good products and some good developers are following what Knuth had to say and are constantly optimizing for speed (but after profiling). Others are engaged in a race to the bottom and are trying to convince everyone else that careless engineering is somewhat better.