It looks like there may have been an internal miscommunication about what was changed. Those specific bonuses which add effects to your auras ("Auras from your skills grant... ") are unchanged. Those are not separate from your aura, they cause the actual aura itself to grant extra bonuses, and as such those are modified if the aura's effect is modified. These bonuses also apply to each of your auras, so if you have multiple auras, each one will apply the stat.
None of those bonuses have changed in any way.
What did change was the way that effects granting extra bonuses not from your auras "You and Allies affected by your Auras have/deal....". These are not stats granted by the aura and have never be affected by changing the effect of the aura - they're granted at the stated value to anything affected by one of your auras. Because these are just granted to objects if that object is affected by any of your auras, these only apply once, regardless of how many auras you have.
These are the ones that have actually changed internally (but not in a way that affects how much bonus you get from them - if you're not using Mantra of Flames, nothing is different).
Internally, these are applied by extra infinite-duration effects - previously a separate one for each such stat, now a single one for all such stats you have. Those effects were flagged to count as buffs*, and so the consolidated single one currently is as well**. This has a mecahnical impact on Mantra of Flames, so was patch noted, but it seems at some point which type of modifiers it applied to was confused.
So taking Commander of Darkness as an example, since it has modifiers of both kind, this has no effect on the "Auras from your Skills grant 3% increased Attack and Cast Speed to you and Allies" stat, but changes how the "You and Allies affected by Auras from your Skills have +20% to Elemental Resistances" and "You and Allies affected by Auras from your Skills deal 30% increased Damage" stats apply internally. There is no mechanical change to the amount of those bonuses you recieve, only to the number of things on you considered "buffs". Unwavering Faith has not actually changed, as it does not have any modfiiers of the type that changed.
*I believe this to have been a bug - they are not described as buffs, and do not display as buffs. I'm pretty sure they were flagged as such by mistake.
**For now. As noted, the original effects should in theory never have been considered buffs. I have an issue assigned to me to review this, and whether there will be any negative consequences to fixing this. The implementation details of how these work behind the scenes should ideally never have been affecting your buff count, and there may be other unintended interactions with some rare modfiers as well.