Can you also answer why something like downloads is in a different order in the desktop dock folder, and not mirror image of the drive?
If that Dock stack is sorted by "Date Added", then the sorting on a backup volume will be different than on the source. That's not a CCC limitation, you'd see the same result if you restored from a Time Machine backup (for example). Apple doesn't allow setting of the "Date added" attribute on HFS+ nor APFS, they literally zero-out any attempts to change that value. As a result, the "Date added" attribute of a file can't be preserved on any backup. If you sort by another attribute, e.g. the modification date or alphabetically, then the sort order will be preserved.
Addressing an earlier comment:
I've been using the version that backed up Snow Leopard previously, and just a few months ago was the last time I used it, and I'd never been asked for it previously.
If you were running CCC on Snow Leopard, that would have been CCC v3, in which case you'd have been prompted to authenticate every time you wanted to save a task or make changes to scheduled tasks. CCC 3 was using a privileged helper tool, but we weren't specifically calling it out by name.