That's not what "an exception that proves the rule" means. It means "you may walk here" implies (proves the rule) there is a rule that you can't walk elsewhere.
In any event, plenty of second systems are fine. It's ridiculously outdated advice. Any time someone replaces their Flask web app with a go or rust version, qed.
I dunno what your experience is like, but I have seen this scenario repeat itself many many times in many places: someone is rewriting something without fully understanding what the old thing did, blindly proclaiming that their rewrite won't have any of the problems of that old clunky thing, introducing new bugs and limitations in the process without adequately solving the problem the old thing was addressing.
All. The. Fucking. Time. Big companies are especially bad at this.
Seems to be a variant of the phenomenon second system syndrome is meant to describe.
That's not Second System Syndrome. That's Joel Spolsky's The Thing You Should Never Do.
Also, I don't think the advice is outdated at all. I've seen it happen multiple times. However, it describes a tendency to be on guard against. It's not some sort of law of the universe.
It's also not about rewriting in Go or Rust (you may be thinking of a completely different piece of advice about not doing ground up rewrites.) The second system effect is about being overconfident from the success of an initial system with limited scope, and being too ambitious in a second system.
In my experience, it means:
"This thing stands out to us as exceptional because it is exceptional; there is a rule which normally applies, but we tend not to notice the rule until an exception to the rule reminds us of the rule by contrast".
Wait... are you suggesting that replacing a flask web app with a go or rust version is in support of or against second system syndrome? That sounds like a textbook example to me - I've seen so many second versions get built mainly for the sake of a new technology that miss a lot of the original requirements that the first version solved just fine.