There is a logic in a madness. Game saves are tracking current clothing pieces that characters wear, so they will not be swapped with by changing customization in the main menu. But the look of each piece will always be customized, based on current customization.
What I would recommend, to keep sanity, is to make customizations first. Then save them in a character group. Then play a new game, with that character group selected.
After this, if you later make new customizations, put them in a separate character group. And manually revert to old group, if you want to check older saves, started with previous customization group, etc...