If you are referring to the baffle tube threads, there is no difference between a MIL spec and a commercial, both will fit. The difference is in the OD of the tube itself. In other words, a commercial collapsible stock will not fit correctly on a MIL spec tube and visa versa.
I don’t believe there is an ‘advantage’ to the flange, purely cosmetic.
Again, be sure you have your tax stamp before attempting this conversion. I can not stress this enough.