That's an advantage, not a disadvantage.
IRV/RCV has one more critical flaw which makes the "lesser of two evils" problem worse: it completely ignores any later preferences on your ballot. If you list your preferred third-party candidate first, IRV/RCV ignores your preference for one first-party candidate over another. As long as your third-party candidate can't win, then your preference gets respected. However, when your third-party candidate reaches the tipping point, it's entirely plausible for your preferred first-party candidate to get eliminated first, followed by your preferred third-party candidate, letting your least preferred first-party candidate win.
That's quite plausible, because it's common for most voters for a particular third party to have the same preferred first-party, while first-party voters more commonly vote for only that party.
That creates an incentive for third-party voters to continue voting a first-party candidate at the top, because in IRV/RCV, only your top choice counts.
That said, hopefully it'll improve the ability to show third-party support, if not actually get third-party candidates elected.