Case length is not really a concern with pistol cases in my experience. I certainly don't ever measure them. Your measurements prove there is indeed a difference between your base and neck measurements. The 40 is straight walled so whatever the number, they should be very close to the same. So, your cases are not getting full length sized. Hope that makes sense. BUT, what matters is if they pass the plunk test in your barrel. If they are falling all the way in and spin freely then they are sized good enough provided they are not loaded too long for the bullet to hit lands.
What I meant about the Dillon dies being the worst is, they have a larger radius at the bottom of the sizer ring so they don't size as low as most other dies. The large radius is there to supposedly assist with cases feeding into it but they feed fine into my LEE and EGW Udies too.