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Players often cast detect evil on NPCs. At levels 1-5 for humanoids, only those with the aura class ability show up.
In several modules I can think of, NPCs detect the alignment of PCs and react accordingly.
It's often relevant to PFS characters particularly that neutral clerics of evil gods, evil familiars and evil magic items with a caster level of 6 or higher detect as evil.

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So assuming lawful good, a level 4 aura vs a level 6 aura wouldn't make much difference? But for neutral cleric with an evil god a level 4 aura would be drastically different than a level 6 aura?
Hoping I understand your question rightly:
A level 4 Lawful Good fighter does not show as Lawful or Good. A level 4 cleric of Iomedae detects as faint for both, regardless of his actual alignment.A level 6 Lawful Good fighter shows as faintly Lawful and faintly Good. A level 6 cleric of Iomedae shows as moderately Lawful and moderately Good. If they're standing next to each other, after 2 rounds, a character using a detect good spell may be able to tell the difference between them.
(Here's a question, maybe for another forum: does "(class levels)" in the table refer to levels of cleric and/or paladin, or to total levels in all classes - for example, edit: for a Chaotic Good fighter 3 / cleric of Sarenrae 3? I think it must be the former, in which case I've done it wrong in one game, but I still see the other reading as possible.)
A Chaotic Neutral level 4 cleric of Lamashtu detects as faintly Chaotic and Evil. A Chaotic Neutral level 6 cleric of Lamashtu detects as moderately Chaotic and Evil. (So, no, the difference is probably not drastically relevant.)
A Chaotic Evil cleric of Norgorber of 4th level shows as faintly Evil, or at 6th level shows as moderately Evil and faintly Chaotic.
Another consequence - an antipaladin has detect good (move action on one target) and smite good (swift action). At certain levels of play antipaladins may choose to smite a PC or not depending on what they see, and they can call information to each other just as players do.