SD cards, and Thumb drives invaribly come from the factory with a Master Boot Record partition scheme and formatted MS-DOS (FAT 16). However, Disk Utility can easily erase the existing partition scheme and reformat them HFS+ or APFS with A GUID partitioning scheme. Assuming Super Duper uses Apple's cloning utility (the only way to create a bootable clone of the later versions of macOS), erasure and reformating is an inescapable result of the cloning process and cannot be prevented.
I think you're missing a step.
You are correct, I was missing a critical step. I just tested using CCC 6.1.4-b5 (7443) and when I selected an SD card as the target drive, I got a popup saying I had to use Disk Utility to change the partition scheme from MBR to GUID. I changed the partition scheme to GUID formatted MS-DOS, but after running the "Legacy" clone it was reformatted to APFS.
I'm pretty sure the card reader is USB.
It is most definitely USB and that is USB 3.1 (5 Gbps). The storage technology used in SD and SD microcards is so slow, a faster connection would not improve the response time or throughput of the device.
