User's choice and decision if and when to do such, not more automation.
Less automation would be very welcome here. Right now TC is doing too much by assuming a certain set of files should be backed up, when in a persistent install, they are highly likely not going to want those files backed up. But even more importantly, I feel I need to re-iterate this: TC IS BROKEN OUT OF THE BOX IF YOU SPECIFY A CUSTOM USER!
Even if you opt to use a persistent home and/or persistent opt does not mean that you should not backup them up.
Let's be honest here, there may be some edge cases where a user might want to do this, but in the vast majority of cases, it is pretty obvious that users are not going to want to create duplicate copies of their data, wait for those duplicates to be created on every shutdown, then figure which instance of their data is actually running - the persisted ones or the restored ones that temporarily overwrote the persisted ones on next boot.
My two cents with love.