Well, as I already tried to explain, the app doesn't look at messages beyond the "messages to sync" setting, and won't be be able to discover that some of them had been removed from the server.
Messages beyond the "messages to keep" setting are removed from the device, hidden or not.
"But desktop mail apps don't work this way, they work in a way that makes so much more sense"
Yes. They can afford to.
My Thunderbird profile (data directory) is ~500 megabytes. This is for an account with about 4,000 messages.
If Aqua did something like this, would I be burned at the stake or impaled?