Hi! Hope you're well. I'm the most recent poster in the LuiAFK thread so I can't actually make a response. So I have to submit a bug report here, I guess.
Are you currently aware of any odd behavior from those "Gathering" chests? I have an Herb Gathering chest in the middle of my Herb garden (Daybloom, Blinkroot, etc.) and it says it's full even when there's a single herb in it.