In my table, this is how I treat the augments for resistance rolls.
Runic inspiration - Yes if applicable runes
Passion - Yes, if the passion is applicable
Skills - Probably no, unless it's been prepared beforehand somehow, like when entering the scene the character is constantly doing the activity like praying while walking in the valley of the darkness, or something.
And yes, I also let the player roll all the resistance rolls where their character is involved in, unless exceptional circumstances.
Addendum: Typically I wouldn't bother having my monsters or NPC's try augmenting resistances, but I wonder how it would work if they did try to do that, as there's only one roll at the resistance table. Any ideas?