Scrapping items give you a reduced resource pay-back no matter what or how you do it. With crafted items mainly guns you can save some of the mods before you scrap them and it might help you save resources. However it often costs something just to do that. Like say for example I have a sniper rifle I love but just found one legendary that has bleeding or has damage bonus that I feel would be helpful. What I can do is switch my costly upgrades back to the low cost 'Standard' version and thus save the more costly mods and then swap them at no further cost to my new sniper rifle.
I sometimes store walls/roofs/furniture into the work bench but, mainly during my first run through settlement. They seem to have things set up when I first arrive in a very space consuming manner. I mean even plants are spread way too thin and I like to consolidate them into more compact rows. Also I do eat up space even constructing say stairs and small floors as I use them as make shift "scaffolding" while I am building up my own house plans. So I just take some time before I decide to scrap furniture or walls etc.. Never know when they come in handy again and I dont like losing the materials already spent.
I have not used the workbench exploit ever and when space gets eaten up or my settlement size is hitting yellow I just lay off a bit and it seems if I give it time the size increases on its own. I dont know what factors into this method.. It may be that I also will scrap other non essentials such as in Sanctuary, I took some time at just going around and scrapping all those picket fences. Also it took me a good few game days just to go around and clear all the buildings of objects.
I have myself not been using my workbench to store items. Items don't seem to transfer by way of provisioner's. I am not sure but what I think is it is just base materials that transfer. So I build a trash can next to work benches just to dump stuff into, Junk mainly. Then when I have time I pull all junk out drop it so it falls in a ring around me and bring up work mode to scrap it all.. This way I have only transferable materials in my bench. I store mods also in my bench but general items like weapons and armor I sort into separate containers. This helps with organizing my items into a fast dump and find system that works better then just emptying my pockets into workbench. Part of my anol item storing method actually drives me to separate, cookable foods from prewar foods, from medical supplies. I even have a trunk for storing magazines so my Misc. section wont get to cluttered.
I was having problems where I was like: ' I know I have a bunch of copper I just collected a bunch, these settlements are connected, so why cant I build a generator?' Then I went to the connected settlement where I dumped a bunch of hot-plates and fuses etc.. Scrapped them and was like "Okay seems like I have copper at my other settlement now.." So this is why I am 90% sure that only base material transfer.