To the best of my knowledge, when you loot gear, one of the mods (armoring, I believe) is not removable. You can customize your gear to a point, swapping the other mods in and out as you see fit. If you want to fully customize the item, you need gear that has nothing in the Armoring slot to start with (which is why crafting produces unslotted items now)
This is true with Sabers, Blasters, and Armor.
99% sure you can overwrite the existing Amoring mod in the gear. You just can't pop it out of gear to abuse the system.
Edit: The reason why crafting produces unslotted items is cost effectiveness: it was a ****ton cheaper for a Synthweaver to make a chestpiece that already had 3 mods loaded in it
rather than to get the Armoring from a Cybertech, a Mod from an Artificer, and the other mod from someone else, nevermind the base item.
E.g. a Synthweaver would essentially get 4 items from 1 crafting, instead of 1 item from 1 crafting.