Take the barrel OUT OF THE PISTOL and try the cases for fit before resizing, after resizing and after loading. If everything fits to your satisfaction the way you have been doing things then keep doing things the way you have been.
Loaded ammunition that sticks up higher in the pistol's chamber than factory ammunition is BIG Deal - a pistol that does not close should not fire but things like a stuck firing pin can lead to a pistol firing out of battery and that is unfortunate.
Your resized cases do appear to be and almost certainly are larger in diameter than never fired brass and there are almost certainly barrels out there that require smaller case heads than your reloads have. You should also check the empty cases and loaded ammunition for over all length the cases and loaded ammunition should be close to the dimensions given in your loading manual. Slightly short cases are common and not a problem - loaded ammunition that is shorter than the book dimensions will in a handgun be higher pressure than the same load with more space behind the bullet. I n a light load there is a
little leeway in a hot load there isn't.
IF you are happy with the current performance of your reloads than keep doing what you are doing until you have problems.
IF you want to be sure your reloads will fit all of the possible barrels then arrange to resize your cases smaller One way to resize your cases smaller is
A must for the serious reloader: EGW offers custom designed, carbide sizing dies that are 0.001" smaller in diameter than typical dies. Not only is it smaller in diameter, the bottom corner is radiused which sizes the case further down. This helps prevent feed failures from cases that bulged near the base during reloading- which is typical of brass fired in Glocks and other loose chambered guns. The dies are made out of carbide.
Undersized Reloading Dies will work with a Dillon Press if they are 550, 650, or 1050. They will not work if they are squared.
I'd be reluctant to say your current dies are faulty if they work. Many makers sell the same dies for 9x19 and 9x21 - mostly they work for the whole range from 9x19 to 9x21 to 9x21 and a bit known as .356TSW and all the way to 9x23 or 9mm Largo - sometimes they don't.
Typically the Wilson case gages are( in some ways but not all) designed to catch any case that is larger than a factory case. Your reloads are larger than a factory load but work just the same in your pistol. To repeat myself you can make your reloads smaller or you can decide they work and they won't work any better so.........