For the most part I agree, just throw your stuff in the common workbench inventory and let it auto scrap for you....but there are a few reasons why it is still a pain to manually scrap.
1- far as I can tell, the workbench only auto scraps Junk - a lot and I mean lot of leather based items are not junk and don't get auto scrapped, so if you are short of leather for armor upgrades, you need to manually scrap gas masks and other really common and plentiful loot that you get from raiders.
When you add plentiful, common, and need to manually scrap as only way to get that leather out, then it is a pain.
2- I am 75% sure of the above but can't say 100% because by the time I realized this, my supply lines had been laid down and it is a major pain to check EVERY settlement in order to test/verify this, to ensure that there are no raw leather and no junk leather to see if non-junk leather gets broken down. But let's say my #1 is wrong, that non-junk is auto scrapped.
In that case then we have problem #2 - if non-junk items are auto scrapped, you have no control over which item gets scrapped. Which means either store all your stuff separately for stuff you want to keep or keep around temporarily, or you manually scrap to ensure you have supply of raw parts on hand so that auto scrapping doesn't kick in.
It's one way or the other - either it auto scraps everything in which case we have one kind of problem, or it only auto scraps junk classified gear, in which case we have the other issue.