How come some shotguns have a mid bead and some don’t?  

And how come most shotguns that I have looked at that have mid beads when I shoulder the gun the mid bead doesn't line up in a figure 8 pattern with the front bead?  

Most of the guns that I have held with a mid bead the mid bead lines up on the lower left corner of the front bead even though the mid bead is perfectly centered in the rib.

The bead closet to the muzzle is supposed to eclipse the mid bead.

The purpose of the bead is to let you know when the barrel is flat. The bead should appear to float above the barrel.

The reason the beads don't line up on the gun has to do with you and how the gun fits you.  Have you ever seen the stock shim kits that typically come with a Benelli or Beretta?  For one of those guns to fit you, you would need to shim the gun to the left.  Think of a wedge thicker on the right side between the stock and rear of the receiver.  It would move the muzzle/front bead to the left when mounted on your shoulder.  This is called adjusting the cast of the stock, you do it left or right.

It could also be you have terrible technique or are some kind of genetic freak.  No way to know without seeing you and the gun together.

The mid bead is a reference point.  Back in the 70's most guns did not have them and if you wanted one you paid to have it added.  These days more guns come with them, but not the cheaper ones.  Guns more likely to be used on wing shooting or clays will come with one.

Why do you have one?  It gives you a consistent point of reference on the gun when you shoulder it.  Different people use them different ways.  On a gun you shoot a lot it is more like a training device, eventually you won't even see it anymore BUT if you start having a problem you can fall back to checking yourself.  The last thing you should be doing with it is aiming it like a rifle with front and rear sights.

In your case, the little bead is telling you something big, why you will hit right every time you pull the trigger.