I have the same problem, but different use case. I don't share my Apple ID. I have two phones and I don't want a combined call log (I want each phone to host their own unique logs). So I have your problem that call logs are shared across devices. Two Apple IDs is non-starter for me.
I found there are 4 things that use Apple ID:
- iCloud
- App and iTunes Stores
- Messages
- FaceTime
The only solution I found is to log out of my Apple ID from only FaceTime on one of the phones. I kept the other phone logged into FaceTime using the same Apple ID. This stopped the call log sharing.
Not sure if others experience similarly. In previous versions I could have FaceTime logged into multiple phones with the same Apple ID and I would just choose different Reached At and Caller ID, and call logs were not shared. Now I only lack FaceTime and some of the continuity functions on the second phone and I can live with that for now.