Yeah there has been intentional inconsistencies to indicate that no two stories are in the same timeline, like Zouken saying the Matou family wasn’t involved in the previous war when they clearly are in this series, and Gilgamesh being summoned by Rin’s father instead of the priest.
It's mostly to keep the timeline from becoming too rigid, which could prevent future writers from telling the best stories that they can. The only thing that never changes is the magecraft system and world building, Nasu is too proud of it to have anyone make tweaks to it lol