Weird, nothing you've said categorically disproves any of it.
Xavier, Magneto, and Apoc all want to preserve the mutant race. Sinister doesn't and never has, he's just a killer. There's no reason to work with Essex, especially since Apocalypse enslaved him in life 9.
It's not necessary for Sinister to want to preserve the mutant race for Moira to work with him or for him to know Moira is a mutant/have the ability to bake her power into chimeras. Working with him may be necessary to further their own goals, or Sinister may have her genetics against her will.
It could be telling that timeline 9 specifically mentions that Apocalypse enslaved Sinister. Heck, that could explain two Moiras - Moira 9 is cloned by Sinister, one of them dies and goes back, while the other remains. Timeline 9 doesn't specify a death, after all.
Moira is not detectable as a mutant. Sinister has no way to know she is unless she exposes herself to him, and why would she? Sinister is from the 1800s and is a villain in every timeline there is with NO redeeming qualities.
We haven't been shown a way Sinister would know Moira is a mutant yet. The book covers a good thousand years - there's plenty of stuff we haven't seen yet. She doesn't need to specifically tell Sinister, either. Maybe it's just public knowledge in the future. Maybe Sinister knows she contracted the Legacy Virus and looked into it further.
I wonder, though - would Krakoa be able to recognize her as a mutant?
The mutants only worked with Sinister and his breeding pits after Sinister killed all of the leadership who would know better. This would obviously include Moira as a high profile mutant leader. She was dead by then.
Do people need to be alive for Sinister to clone them?
You're reading too much into Cardinal. His pacifism is a reference to Nightcrawlers faith taken to extremes- nightcrawler being extremely religious has been a theme with him forever. The hive mind stuff is similar to powers the stepford cuckoos have, and sinister introduced that flaw intentionally to kill the mutant population. Theres no need for Moira here and trying to insert her powers is nonsensical.
Yes, those are other ways to explain Cardinal or the Gen 4s. There being other reasons for the Cardinals and Gen 4s being as they are doesn't mean including Moira genes is invalid.
I'm just spit balling here, man. There's no need to get all weird and dismissive. I appreciate that you don't think this is what's happening. It's probably not what's happening, but it's fun to think about.
I hate to be dismissive myself, but this doesn't work with what we currently know - Destiny said that if Moira died before her mutant powers manifested, she'd be dead for good. It could be revealed later that Lifetime 6 was Moira testing this and killing herself prior to age 13, but the reveal would probably revolve around why it still worked.