I know what you mean but magical and non-magical B/P/S damage is not defined as such.
The resistance you mean is B/P/S damage from a non-magical weapon. Any source of damage that is not a weapon bypasses that.
So yeah, in the case of a needles fireball, make it damage from a non-magical weapon.
I’m sorry for being pedantic. I hate these rules too but this is how they’re written. Pathfinder 2E ends up a lot simpler if you use a VTT (Foundry VTT is amazing, and has no recurring costs).