Yes, this is where, in practice, I've seen the adage used incorrectly. Even when Knuth isn't quoted directly, the idea that "premature optimization" is inherently a bad thing has led many a web developer down the path of terrible architecture decisions. So I understand Duffy's point exactly.

It's not that all issues are preventable. It's that you can prevent a lot of them with just a little extra work up front.

It's a misuse of Knuth's original point, which has much more to do with how brittle and incomprehensible "optimized" code can become.