What is the correct translation of "Thanks for confirming"?
Gracias por confirmar (futuro)
Gracias por haber confirmado (pasado)
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Technically, yes, in the past it should be gracias por haber confirmado, but that doesn't mean you won't hear gracias por confirmar with high frequency with that meaning.
For another example, you'll hear gracias por venir all the time, even though, presumably, if they've already arrived at your house/party/event/place/shindig, you're thanking them for having coming over (they're not on their way by the time you're thanking them). Context normally makes that pretty clear, but when it doesn't, using the infinitivo compuesto lets us clearly indicate a prior action.
If you feel the need to strictly distinguish and force a future interpretation, in your specific example (not necessarily applicable to all verbs) you might say gracias por confirmar con antelación / de antemano or similar to avoid any confusion.