.003 is the norm for neck to chamber clearance, I'd say you're in spec. Make sure your seating die is not screwed down far enough to add any crimping, otherwise you could shave the bullet in the last ..002-.004 of seating as the die is trying to crimp at the same time it's finishing the seating process.
The outside diameter of your fired brass has a little springback after firing as the brass remembers it's original diameter somewhat. I really don't see an issue with the neck dimensions in any of your readings.