Piclone (gui) only backups the actual data - https://github.com/raspberrypi-ui/piclone
To run from command line
Copy this script https://github.com/raspberrypi-ui/piclone/blob/master/src/backup
On raspberry pi, run
sudo nano sdclone.sh
paste in the text
cntrl-x then y to save and exit
sudo chmod 777 sdclone.sh
I'm using a Sandisk external SD card and USB micro SD card reader
16gb Sandisk class 10 Micro SD card - https://amzn.to/350eGpw
Kingston Micro SD card reader USB - https://amzn.to/2Ver1BX
Run lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sda 8:0 1 14.9G 0 disk
├─sda1 8:1 1 43.2M 0 part
└─sda2 8:2 1 14.8G 0 part
mmcblk0 179:0 0 7.5G 0 disk
├─mmcblk0p1 179:1 0 43.2M 0 part /boot
└─mmcblk0p2 179:2 0 7.4G 0 part /
To run
sudo ./sdclone.sh /dev/sda /dev/macblk0