This is global application setting (Preferences), not per-project, as having it per-project makes no sense (you would need to re-open every project ever saved and change the setting and re-save it).
Instead you just set it ONCE and it works for all projects without worry.
This setting does NOT mean that formula is not saved in .APX file. It IS saved, but it is NOT loaded from .APX when more up-to-date version of the .AFL formula already exists on your disk.