it's that I'm under the impression that once you use $1 once, perl needs to track it for every regex in the entire program...

You're thinking of $&, $` and $'. They are always set by all regexps when they are used anywhere in the program.

$1 .. $9 are always set by every regexps that succeeds. When a given regexp has no corresponding capture, they are set to undefined. No attention is payed to whether $1 .. $9 are used anywhere.