Interesting point.
That's not the only legal eyebrow raised by Bush v. Gore.
But we already know one such incursion, even by SCOTUS doesn't completely eliminate stare decisis, even if it portends to violate it, or holds open the prospect for violating it in the future. Perhaps we can call it a contingent violation.
However, let us please note that stipulation you have so wisely cited here, may be binding on future high courts rhetorically, but not so legally.
Any future SCOTUS is free to rule within bounds of law, no matter what pretense Bush v. Gore promised or implied.
To the contrary, as you so keenly point out, if they ever conflict, it's the Bush v. Gore stipulation that should fall, not an otherwise lawful high court ruling.
But thanks for the thoughtful, learned point.