The writer of that episode claimed the Nepenthe episode was his favourite Season 1 episode, so I don't think it was meant to be a negative message towards the episode.
Whether it was intended to be or not, it came off that way. The anti-season 1 and 2 fans took it that way and it gave them validation. Given the storyline of season 3- rewriting the way they felt, Deanna playing mind games with Riker's feelings, basically ignoring Kestra, everything being about Thad after they seemed somewhat at peace in season 1- and hearing Matalas say he had issues with how they were portrayed and that he wanted his take on it, it seems pretty obvious he wanted to undo that episode and hand wave it away as much as he could.
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