Although I'm almost certain that it's been suggested at least once, if not multiple times, a thought that comes to mind is the idea of adding in a "shop" to the wayfort vault that you can "sell" unique items to in order to store them, and then you can buy copies of them back from the stop once the item is "in stock" after you've sold it. Although this is likely excessively complicated and requires a lot of flag-checking work, which would probably bog things down.
An alternative idea would be to expand upon the Forge Golem NPC, possibly having something where they're freed and relocated to our wayfort vault to serve as a guardian and smith there since their current residence is, at least per my memory, abandoned and isolated with very little plans in motion lore-wise. Then the Forge Golem could be given a shop that sells unique items based upon quest completion, which may once again be complicated to implement but it might be somewhat easier than the first idea since it would just be tied to the already existing questlog instead of having to create an entire subsystem to check on what unique items the player has activated.
The main reason this thought comes to mind is that, although many of them collect infinite dust in the already existing storage, it's rather difficult for me (and likely many others) to truly let go of unique items due to the fact that, as has plagued RPG's for nearly their entire lifespan, I might, maybe, need this particular item later. So having a shop specifically for lost unique items somewhere in the game would be nice.
I know that console commands exist and it's easy to just check the items pages on the wiki in order to re-add them to my inventory, but I wanted to suggest a system where people who don't want to dip into the console menu don't have to if they don't want to.