So ill update this as i go alone but i have a lot of questions that im trying to answer for myself, figured that i could help some others looking for answers as well.

1. If you do the red remnant start than the queen will not be in the vault. I wanted to do this start with the intent of eventual saving the queen so i swapped her out for another warrior. however she wasn't there after i did a mad dash of death and managed to make it there with a single worker and ran inside to look.