It seems to me that a trilogy isn't necessarily the first three films that are made in a franchise, though this is certainly true for the first three Bourne movies (notice how the last shot of the third movie mirrors the first shot of the first movie).

As for the Godfather movies, I won't comment, as I still haven't seen Coppola's final cut from 2020 of the third movie, now titled The Godfather Coda: The Death of Michael Corleone.

As for the Indiana Jones movies (not mentioned in this piece), I offer a "radical" idea: the real trilogy doesn't comprise the first three movies that were made. For more on this from me, here you go: https://lyonsnyc.medium.com/indiana-jones-and-his-five-adventures-89fdbbcd049e