Don't worry. I'm mainly just venting frustration since Robobob's disappearance means that that these things likely won't get fixed.
Changing a sprite display behavior might not be a big deal but 1. sounds like much more than that. A single item stored in a stockpile probably always gets turned into a container before storage. Changing that would require changing plenty of other places, and any additional place raises the chance I could introduce bugs...
It's not just inside piles. Even right after appearing items already appear as pile.
However, when it's being carried, the proper item-sprite appears.
2. How is that a problem? Piles are sort of like transport containers, so I wouldn't be surprised if they're programmed in similar ways. What would you change?
You should try it out and see what happens.
The gnomes go kinda crazy; they never pick up the items and instead just keep walking to an empty spot in the nearest stockpile.
They show the same strange behavior for 3.
Number 4 is definitely difficult, but maybe there is something obviously wrong.
I'd probably look how new items are generated from workshops, farms and mining.
Since the bug doesn't happen with straw and stone, any difference compared to workshops could be the culprit.
While I'm at it, here's another big one for me.
I remember that in the past, more enemy kingdoms would appear similar to merchant kingdoms.
I don't know if it was with growing kingdom value or passed time, but apparently this is bugged/was removed.
If the code is still there, maybe you can reactivate this feature.