There really is no difference, other than the types of devices that are allowed to be a member of the list. The Hunt Group extension lists are different, as they allow off-node devices to be included as members.
I like a clean database, and kept things consistent so I would know where to find them. I never used the Phone/Voice Processor list unless there was actually a voice mail device as member of the group. All hunt groups were in the Hunt Group extension list area. Everything else, such as page zones, were in the IP/Digital Phone area.
What the installer did is not actually wrong, just sloppy in my view.