So, from what I understand, originally Varian was supposed to be in S2 more. Not as in "he went with them on the journey," but as in "looking in on Corona to see what was up with him." The fact of the matter is, his role was lessened because the fans loved him so much, but that's not the character the executive producer wanted people to love. He wanted everyone to love Cassandra (his personal favorite). So, out of literal spite, he removed Varian's parts from S2, minus his ten second cameo in "Happiness Is..." that wasn't actually him.
As for what happened to getting him the help he needs? IDK, it's 100% in Frederic's personality to just shut problems away and ignore them and hope they go away. We don't know why he didn't actually make any attempt to help Varian. Or, if he did, why Varian refused it until Frederic gave up.
As for Andrew, I never personally headcanon that he was literal cellmats with Varian. We've seen before that they have tons of empty cells. So, I think they either had adjacent cells or cells right next to each other. Some way they could communicate with each other easily, makes plans, etc. But that's just my headcanon. The text of the series is that they shared a cell.
As for whether or not Varian was okay? Not really? lol Like, I don't think Andrew threatened or harmed him in any way, but he definitely manipulated him, convinced him to give into his revenge fantasies, convinced him that using Saporian magic/alchemy on the king and queen and all of Corona was a good idea. The fact is, their relationship was a lot more topical than was likely intended. Varian was basically indoctrinated into an Alt Right type mindset, and Andrew used flattery, understanding, and compassion to get to him. In other words, all the things that Varian felt his life was lacking.