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Much of the previous discussion and decision to not allow such customization stems from the fact that specific arms and armor being altered/upgraded makes them custom magic items, as these items do not follow tight cost formulas like standard magic arms & armor. Custom magic items are not meant to be purchasable by PCs as part of access through Prestige. Because of the way specific magic arms & armor blend wondrous item effects with standard enhancement/enchantment effects it's too tricky to from a cost vs. power level perspective to adjudicate outside of a case by case basis.
There has been talk of including upgraded/variant versions of specific magic arms & armor for access on Chronicle sheets, as this would allow careful weighing of the cost vs. how changes might change the balance of the item. I also imagine several higher level modules sanctioned for society play will occasionally include such items, which means they will be available for access through play of said modules.
I do agree with you that the flat-rate enchantments should be do-able, but I also understand that the sheer amount of potential combinations even with just these enchantments (and any further enchantments of the same kind in the future) create too many possibilities. Let's not forget how stupid cheap some rather game breaking items were in D&D 3.0 because of an attempt to make their costs purely formula based.(Boots of Striding & Springing, anyone?)