All of those things would definitely bother me. My yearling is prone to choke so I have a sign on his stall door that specifically says, "Do not feed me treats - I choke!!" Maybe you could do the same? I definitely don't need him choking while I'm not there. No one at the barn would even know what was happening, unfortunately. That and my yearling tends to get lippy with treats. I don't need someone teaching him bad habits and me having to constantly correct them.
Have you asked her why she cuts his stall off during the day? If you pay for it, he should have access to it 24/7. Your horse is suffering at her expense, unfortunately, because it seems like she wants less of a mess to clean up. As long as the shavings aren't dusty and there's good circulation in the barn, there should be no respiratory issues there.
Hope you get everything worked out.