Sorry I'm late here. Haven't been really active lately (still depressed, TBH).
I took that post rather differently.
First, I don't think it was Polar implying that GS isn't part of Nintendo's history. It was Polar's source giving their impression of what Sakurai and his team thought, if I understand.
More importantly, though, the way those statements are phrased make me think that the choice of making Isaac an AT and possibly even a costume was made BEFORE the Ballot results came in. Because it was "regardless of his popularity". Had his popularity been known or defined then, it feels as though that would have been phrased differently. "Because his popularity was not sufficient" or "in spite of his success on the Ballot". So, what if that wasn't about the Ballot at all? What if Sakurai saw the reactions to Isaac not returning as an AT, and decided immediately to include him as an AT? The costume may then have come about because of the Ballot, or because of that same small vocal fanbase.
Undoubtedly more importantly, though, is the idea that Nintendo was shocked by the reaction to his exclusion. Because that's another data point in Isaac's favor, and it's something else that would have slipped past the Ballot: People who did not vote for Isaac still wanted him in the game. Since K. Rool was confirmed, we've seen massive outpourings of support for Isaac from their fanbase. In the leadup we've had Shadow fans, Geno fans, Lloyd fans, etcetera. All coming out to support the Golden Boy, but none of whom voted for him. So the fan desire for him is even larger than his placement in the Ballot.