That's some amazing work, @joshua_keyes! It's nice how you've used Tiled to also verify that your assets would actually work to recreate a game like this. Thanks a lot for showing this!
And thanks also for your suggestions! I like all of them and definitely would like to add the mentioned features. About the confusing object selection, indeed Tiled allows you to select objects on all layers. This is most of the time the expected behavior I think though. What would definitely help I think would be some hover feedback so you would see before clicking what object you're interacting with.
I've opened issues #1188, #1189 and #1190 based on your feedback.