Working with APFS Volume Groups from the Carbon Copy Cloner Knowledge Base explains the underlying APFS structures that are enabling the new OS architectures and if you scroll down to the section on
Finder shenanigans with the Applications folder you will find an explanation of how and why the file count varies.
Boot Volume Layouts and
Layout of the Catalina Boot Volume Group (both from The Eclectic Light Company) help explain what you are seeing in Catalina as well as answering some of the questions about why there is a big cloning issue in Big Sur and
this Apple Developer News article explains the rationale behind the changes in Big Sur. Absorb all of this and you begin to get the full picture of what this all about, how it fits together, and how, through the actions of "firmlinks" the system can contain elements from both the data and system volumes and reaches a zenith in the
boot volume in Big Sur which is essentially a "virtual" construct".
Looking at this in total, it appears that implementing any "cloning" ability in Big Sur may have to include
installing the boot volume using the MacOS installer, or at least portions thereof. I am not holding my breath waiting for that to appear.
