No, there is no secret ending. Yes, the weird fourth wall breaking and Truman references are still intentional.
The point is, Mike Wheeler the storyteller is unhappy with his ending, and that's why he's a storyteller. He'd rather write fiction than live his reality. He is the narrator of this story, and always has been. He has little to no interiority because he's not supposed to be a character in this story. He's just there. Will and Jane are the main characters.
The show always used recurring door imagery and metaphor, and we are told quite explicitly which doors Jane, Mike, and Will chose in the end. Jane chose the first (death), Mike chose the second (acceptance of fate), and Will chose the third (escape).
Jane represents childhood magic apparently, and although I feel her character was done injustice, I can dig a character being tied to an allegorical concept. So really, that means Jane was an allegory in Mike's story. Perhaps representing childhood wonder, first loves, and innocence? Therefore her death signifies the loss of childhood, and even the death of love itself.
Mike imagines an ending where She (magic, wonder, love) lives on. She's free but she's also isolated. On her own like that, it's not so different to being kept in Mike's basement or Hopper's cabin. Mike must associate something very shameful to these concepts, otherwise he wouldn't constantly hide her away in his story, despite loving her so much.
Still, he wants to believe in this alternative ending where Jane, who is love, and innocence, and magic, lives on in relative peace. He implies that simply believing it can make it true. Will believes too. They share a meaningful look before being interrupted by an opened door, and it's their last ever interaction on-screen.
No, there is no secret ending. There are many endings, and it's just that we've only been shown one of them. The bittersweet one. Mike killed magic, first love, and childhood wonder. Then he gave Will the good ending. Mike thinks the good ending is having Will no longer love him, and sending him far away from him.
Finally, he chose the second door. This means he didn't write the ending he wanted, but the ending he felt he deserved. He will never tell the true story of the mage. As in, he will never clarify what Jane actually represented, and what her death truly meant to him.
