One solution would be to turn off the prefs option, and then have a script add-in which adds the title to listers that come from layouts. That way all of the special titles would be set via the Set LISTERTITLE command, and they'd all be saved and restored when restarting.
This script shows an example of how to run commands when listers open, and how to look at the layout name when running them. It does some other things you wouldn't need, but would be a good starting point:
If you need more detailed help on that, please link your account.