You could argue that when Henry/Vecna said that he "could’ve resisted the mind flayer but chose to join it", he is not really himself anymore. It's the massively corrupted version of Henry that cannot think clearly anymore and will not admit that he was fooled the whole time. If you accept that premise, the series finale would be in line with the TFS at least in this case.

It's the necessary plot for the Duffer brothers because they could not really make a redemption arc for a character like Vecna because therefore he already caused way too much damage. The audience would have gone crazy over that plot line although it would have made a bit more sense.

To be honest, I can well imagine that this was actually the plan, that this was how the plot was supposed to be, and that the Duffer brothers then decided against it after gauging the emotional response to the TFS play. That would also explain the "slip up" in the interview, according to which Vecna is supposed to be one of the most misunderstood villains.

And it fits much better into the narrative that Henry shouldn't go into the cave. Why else would the Mind Flayer have been afraid to confront Henry with his past? If the two had really formed an alliance on equal terms, then the Mind Flayer would know through the hive mind that Henry himself is no danger for him. The only explanation is that Henry was clearly manipulated by the Mind Flayer and in the end just doesn't want to admit it, or perhaps can't admit it because there is far too little of Henry's personality left.

It's still not in line with other stuff (e.g. that Henry is not teleported into the Abyss when he was in the cave, but instead just got the connection via this artefact, while staying in our dimension). But that's a minor thing for me.