Loadouts are a bit of a pain to use, some suggestions:
Update: Update current loadout to match current gear. Instead of requiring a delete and re-set.
Upgrade: When an item upgrade is alchemized, put the new piece of gear into the loadout, instead of wiping loadouts using this item.
you can overwrite the loadouts, so you don't have to delete and create a new one every time you want something changed.
updating could be a bit impractical for people who change their gear manually almost every time. as a toogle it's ok.
yes, alchemized items should go into loadouts automatically.