Wait hold on, the one who actually stopped time is the God of Time, not Arnos?
Oh wow, at first i thought stopping time is just another step in Arnos' plan for the Sisters, but now looking at it again, with how the time is paused in the middle of the Sisters' search for roots and right after that they suddenly stopped and look around confused, the Timestop could be some kind of Arrival Sign for that God.
Now, with the correct fact in mind, i can't help but think that this is all still within Arnos' plan. With the arrival of the Time God, who would stop time to prevent any attempt at changing history, it would result on ironically giving even more time for the Sisters to search for their roots, while of course Arnos keeping the God company.