If you have SD set to do a Smart Backup, it will only copy changes made to your internal since the last clone. If you do a full backup, everything is overwritten. Smart Backup is by far the fastest and easiest way to do this. In either case, I don't see why your user Library isn't duplicated in the clone. Have you contacted David Nanian, the developer of SD? In my experience, he has been very helpful.
Jon
macOS 11.7.10, iMac Retina 5K 27-inch, late 2014, 3.5 GHz Intel Core i5, 1 TB fusion drive, 16 GB RAM, Epson SureColor P600, Photoshop CC, Lightroom CC, MS Office 365
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