After reading every post in this thread in an attempt to solve this, I think there is a big communication issue in referring to Apple ID's in general when they come in two variations. I believe that some people on here are referring to a main Apple ID and some are referring to sub accounts or aliases under a main Apple ID. Not to mention the fact that your Apple ID could be one thing for iCloud backups, another for the iTunes store, another for iMessage, etc...
Let's say we're exclusively talking about the Apple ID's for iMessage as that is what this problem is referring to. The posts saying "don't share an Apple ID, change that to solve the problem, doing that is wrong" would be correct in that you should not simply share one main Apple ID between different devices for different users in regards to iMessage. However, there is the scenario where you create an Apple ID, say it's called ID 1, and then sub accounts under that ID, say they're called Sub 1, Sub 2, and Sub 3. Let's then say you have a Macbook the family shares, an iPhone exclusive to one user, and an iPad that the family shares. I have this basic scenario myself and was told over the course of a few years by Apple reps in person and through phone support that having them all sign in with ID 1, then having each individually use the sub accounts so that Macbook = ID1 Sub 1, iPhone = ID 1 Sub 2, and iPad = ID 1 Sub 3 for iMessage is appropriate and will be successful. Side note - This is my setup for iMessage; all use different ID's for iCloud backups.
This has been the case until iOS 12. So, before I would get a separate iMessage text thread between each device. Now they come through randomly under the same thread. I would additionally argue that this is in fact an Apple bug rather than expected behavior based on incorrect user use of Apple ID's because there is no consistency. ID 1 Sub 1 and ID 1 Sub 2 devices could both send messages to someone and come in overlapped in one thread, while ID 1 Sub 3 sends one that comes in separately. And the messages coming through in one thread, the contact showing, or otherwise is seemingly random rather than consistent.
If Apple wants to discontinue support for the feature of having sub ID's under an Apple ID, then that is their choice. However, as it is still supported and a viable feature, this should not be happening.