War Department clerks created all the duplicates and multiple listings under similar names a century or more ago. The NPS simply reproduces entries that existed in the original card index system.
I've noticed some of the new features you mentioned in the NPS system. Up until now I had assumed they were still working on the software. I've not been able to find anyone in the NPS system for at least a week. If this is a permanent change, it will make research a lot more difficult.