I've been taking items that I don't want to scrap (either because I like the item, or like you, they have the higher level components and I don't want them scrapped for low level components by accident), and storing them in containers that are NOT workbenches.
Example:
I really like the look of the skull bandanna you can wear on your face, but I really like wearing the gas mask as well and usually wear the gas mask. I store the bandanna in a metal box I crafted and keep next to the work bench.
This is also true for a weird alien toy I found, my vault uniform, and my wedding ring.
It is by far not perfect, but a quick fix.