My lightning protection and poison protection are 425 and 394 respectively when holy aura is active. However when I put 1 point into Shelter from the storm (+1 vitality and +15 elemental protection) they go to 415 and 331 …hmmmm. Other elemental protection and vitality stats are affected too I just chose those 2 as an example. It seems when you add a point to shelter from the storm its overriding the base vitality and elemental protection from the skill itself.
Id also like to point out you seem to keep the base buffs from holy aura even if you swap it out for another skill until you change screens. At least its displayed that way on the character sheet.