To be honest I played in a server with latency issues, and it turns out I can actually place items in the vessels, lockboxes and display cases when I'm not lagging. Should have tested in singleplayer first, oops! I suppose my only remaining issue is with the book shelves and bowls then.
Went back and tested this one too and it turns out that all items have hitboxes when shift-clicked, even bowls! (even though it's very shallow) So it wouldn't be as easy as I thought to categorize items as with/without hitboxes. Maybe it's as simple as allowing shift-clicking but not the infinitely stackable items like firewood, peat, ingots etc to prevent them from being used as blockades or step-ups.
Thank you for linking me to this thread, it's definitely got some interesting ideas. I'm more in the camp that the spawn-protection is mostly fine besides being unable to place things back where you found them. That's the only thing that took me out of the immersion.
Yeah this is definitely a valid concern, and not just from a coding perspective but also a clarity perspective. If there are a bunch of exceptions to what can and cant be placed then I can imagine it would be confusing for players.