The trick to making SharePoint backups easier is to forget about SharePoint. Ignore the databases, ignore the files, ignore the configurations, ignore it all. Instead, simply back up every block of disk space. As data is changed, that data is written to disk in the form of changed disk blocks—have an agent on the server grab those changes and send them off to a backup repository.
Those backed up disk blocks can also be time-stamped, meaning the Backup 2.0 solution can keep track of which changes came from what point in time. That immediately solves the problem with keeping the configurations synchronized with the content; so long as you’re grabbing all the disk blocks up to a specific point in time, you’ll have a consistent SharePoint restore. That also means you can choose to restore up to any point in time, effectively “rolling back” SharePoint to some earlier point in time, if needed.