As of bug 7410 we only offer to migrate .hconf files in tl-setup. The following non-Hiveconf files are marked as configuration in the spec files:
A few of these, like tlclient.conf might need migration if the admin modified it and the defaults were changed in the new version when upgrading. In the cases where migration would be needed it's easy for the admin to miss this.
As of bug 5773 we no longer move away and rename an existing configuration file in favor for the new file when a conflict arises. In some cases this can lead to a broken system if old configuration values aren't valid anymore. And the issue gets worse since it's easy to miss the need for migration here.
When fixing this bug we need to remember to update our documentation for configuration migration.
One improvement in this area could be to list these files in a separate list in tl-setup, highlighting that they might need to be migrated.