The Woman's purpose
I think that Mother did indeed orchestrate some of what happened in the movie but not everything. Her goal was to eradicate all humans except for the ones she raised. Woman had a hidden purpose that she didn't know about. This purpose was to bring any humans she found back to the facility to be killed. This is why she kept asking if there were any others and why there was a welcoming party when Daughter returned. Woman did find other humans, but they all died in other circumstances, it seems. Once mother confirmed that Woman was alone, she found her and killed her in the last scene.
I don't believe that Mother intended for Daughter to ever escape, but once she saw that Woman was desperate enough to harm Daughter, she let them go so that they could hopefully come back with others.