TL;DR - Evernote Tech Support says this is "normal" behavior, but don't say why this is a desired function.
Longer version - After some back and forth with tech support they confirmed that this odd/stupid behavior is by design. Confirmed by "Senior Technicians". Below is the final response I got back from support.
"Thank you for your response. I've consulted again with our senior technicians here. From their understanding, the behavior that you are seeing is currently intended.
Again, I certainly understand the frustration and inconvenience from this process. I will make sure that all of the information that you have provided here is passed along to our product team for consideration in improving for the future.
Thank you for your response. I've consulted again with our senior technicians here. From their understanding, the behavior that you are seeing is currently intended.
Again, I certainly understand the frustration and inconvenience from this process. I will make sure that all of the information that you have provided here is passed along to our product team for consideration in improving for the future."
I guess I'll either switch my people to another product or figure out how to automate a script to delete it.
Kizan