I think I could make a slight change to BCE and this would all work. All the plumbing for something like this is already there.
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There is some similar extension for PFRPG2?
Disabling it works well.
As I looked through more things that have auras I am seeing more of the edge cases you alluded to. As you said different auras have different rules around when and how often a save is needed. I also found some where the aura is nullified if the aura owner is hit by someone affected by the aura (Archon Hound - Aura of Menace).
Overall I think you are completely right. Too many edge cases to code this for automatic saves.
Had time to implement that this morning. See v1.4.