Yes, you can do it with CCC, which performs a filesystem-level copy of the drive and creates new preboot volumes required for bootable APFS drives. However, you cannot clone it with Apple's own disk utility because it fails to properly reinitialize the preboot volumes and thus fails to produce exact clones or even restorable images of APFS-formatted drives. ....
Actually, it turns out there IS a way to clone bootable AFPS drives BUT it is FAR from obvious and requires multiple steps involving creating a Disk Image first.
I FOUND THE SOLUTION by using first creating RELIABLE disk images of APFS drives. It was not easy to figure out. The ONLY path is to make a viable re-usable disk image formatted as APFS and use it as a Restore image or clone, as follows:
1. First create a blank image file formatted as APFS and Read/Write (requires pre-determining size of image file).
IMPORTANT NOTE: The image (destination) cannot be stored on the same drive or partition (source) from which you are going to create the image.
2. use Restore from <volume> to clone to newly created image file
(Highlight destination <volume> then click [Restore] button and select Restore From <volume>.
3. convert image file to Compressed format (Image > Convert).
4. Now you can use this image to Restore to any APFS volume (I have not been able to restore to an HFS+ volume). It contains all the proper "sub" volumes (Pre-Boot, Recovery, VM).
ONLY THEN do you have a reliable APFS image AND clone, especially w/bootable macOS. I have done this repeatedly and it works fine.
ANY other options/paths, are greyed out, yield "Resource busy" or "image is not APFS format" errors or produces image that is not reliable. Even using Apple Internet Recovery tools/boot was the same.
NOTE: you do NOT need to do ANY of this using Recovery tools. You can do this from a live boot of macOS drive. If you do not have a destination to store the image file other than the same internal drive, you can create a partition large enough to store the image file, using Disk Utility. And yes, you can partition macOS boot drive live.
CAVEAT: Tested only using Mojave 10.14.4 on 2019 27" i9 iMac w 40GB RAM and 512GB SSD (no T2 chip), so YMMV.
Apple needs to fix Disk Utility to work straightforward like it used to but with better support for APFS.