You sure? The first volume of the novel was published in 2022 while the first manga volume came in 2023 so it's not the case of it being adapted to manga first either.. The differences you mentioned are likely caused by the mangaka adapting the novel instead of the webnovel.This series is in an interesting position since it has no Light Novel and was directly adapted from the Web Novel.
However it seems the Mangaka has free reign to do whatever he wants with the story since he added stuff that was not in the Web Novel like Yuri meeting the Saintess last chapter which never hapened in the Web Novel.