Allow me to ask you: Why wouldn't they already be? Madame X concluding so, our crew believing so, all the info at Zeight, and our form change at the Puppet Master fight - these all should prove we already are.
Also, if the MC or Crescent were to perish, would the other perish as well? They have a host co-host relation after all.
I believe it's just as you say. And Spacea and Tiempa's higher up may be Griselda (who may be the Giratina we've seen several times in the story).
EDIT: Totally forgot that the space-time duo fought against Griselda in the past, so Griselda can't be it. (Thank you to ICSW for reminding me! You say Variya could be the boss, and I could see that happening. )
About the Archetype: You question where the object is, but I think our light quartet together is now the Archetype. Recall what happened in Eclysia Pyramid. Their bodies shone as light and they came together to form the Archetype.
I think this was referring to what the fourth text was saying. People react to the Archetype in their own, different ways rather than the Archetype literally choosing who lives and dies. Some people had their primitive instincts reawakened and turned into legendaries. Anathea, I believe, initially had dark-colored hair and after the influence of the Archetype, she had golden blonde hair. I'm inferring she kept the alteration because when we meet her in the past, she had blonde hair.
Well, that was fun. Thank you for all the time you spent writing this! The in-game texts you provide are very helpful.