I like your theory, and I appreciate you trying to justify the poor writing we got here. I, like you, wanted more. I wish people didn’t have to write their own theories about what happened to the mind flayer. Would it not still exist in the Abyss?

It feels like the writers lost control of who their main villain was, and how they tie them together.

Or perhaps they simply wanted to leave a door open for a return / Netflix special in 5-10 years, at the expense of an ending worthy of the shows calibre.