One thing I learned from 4/his/ was that threads could last multiple days and even a week sometimes, and because of this they just turned IDs off. I guess it was actually more confusing leaving them on since IPs would change over the course of a day as people changed locations.
Not having a persistent thread ID until the end of the thread is annoying, and the longer a conversation continues the harder it is to follow. Since tripfagging is manual and it's annoying to do a new tripcode for every thread, it's not a practical fix for this issue.
A voluntary option to store a thread session cookie is a way to fix this. The settings interface should provide a way to delete individual thread cookies if desired. You can debate whether or not the cookie should be opt-in or opt-out but personally I think it should be opt-out. That way newfags won't easily samefag.
Also consider how this feature would interact with flags. It's probably not fair to reveal someone is using a VPN when their flag changes but not their ID, so I think the cookie would need to store the original flag for the public post. Moderators may need to see the real flag on their end.