Hmm, yes I see what you mean. After testing, "nearby allies gain ATK: 1" aura for my player's pirate captain PC, to properly buff other PCs and neutral/yellow pirate PCs would require two effects (posting in case anyone else could use it):
AURA: 15 friend; YARRR; ATK: 1
AURA: 15 foe; YARRR; IF: FACTION(neutral); ATK: 1
I don't mind the player having to click two effects (easy), the only drawback I could see is that if we play with aura applications/removals visible, it would also harmlessly apply the ATK: 1 effect to red/hostile creatures in the range, though they wouldn't actually gain the benefit, which might just be confusing to see in the chat/combat tracker. However since we haven't actually played with this extension yet, maybe we'll find the notifications spammy like you said with the Aura of Protection and just choose to hide them all anyway.