Why is it matching the final " if it could leave it for "? and the pattern would still match?
In the greedy case, it's because that's how regexes work; if .* can match the quote ("), it will. Note that it would be different if the trailing quote was non-optional; then the greedy match would only match up to but not including the final quote.
In the non-greedy case, of course, it's the same problem; the non-greedy succeeds by matching nothing at all, as the optional final quote does not have to be matched either.
Here's another way to look at the effect of a "non-optional" final quote for both the greedy and non-greedy cases:
$string =~ s/\"(.*)\"/$1/;
# <= Final quote " pushes left against
# otherwise greedy match (.*)
$string =~ s/\"(.*?)\"/$1/;
# => Final quote " pulls right against
# otherwise non-greedy match (.*?)
So when the final quote is optional, neither of the above constraints get enforced; the greedy match can be maximally greedy, and the non-greedy match can be minimally greedy.
And by the way, you don't need to escape the quotes in a regex. \" can be just ".
s''(q.S:$/9=(T1';s;(..)(..);$..=substr+crypt($1,$2),2,3;eg;print$..$/
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