CCC 'Standard Backups' do not include the operating system
By default, CCC does not back up the read-only "System" component of the startup disk; that part of macOS cannot be restored, it can only be reinstalled by the macOS Installer. When you configure a backup of your startup disk, CCC will back up the contents of the Data volume. That's all of your data, all of your applications, and all of your system settings – everything about your Mac that is customized. You don't have to be able to boot your Mac from the CCC backup to restore data from it. You can restore individual files and folders using Finder or CCC while booted from your production volume. If you ever need to restore everything from a non-bootable backup, you can install macOS via Recovery mode (or acquire a replacement Mac), then migrate data from the backup via Migration Assistant. CCC backups are compatible with Migration Assistant, and we support that method of recovery alongside numerous restore options within CCC.
Why aren't the Apple applications on my backup disk?
If you compare the Applications folders on your startup disk and backup volume, you may notice that a couple dozen applications are not present on the backup volume, e.g. Mail, Calendar, and all of the other Apple-provided applications that are installed as part of the macOS installation. These applications are actually located on the read-only "System" volume. Because these applications are stored on a read-only volume, they can't be modified by you, nor affected by malware, nor can they be restored — they can only be reinstalled via the macOS installer. As such, it doesn't make any sense to include these in a backup. Note that this does not affect the backup of the data that is associated with these applications. All of the data associated with these applications resides on the writable partition of the startup disk, and CCC backs up all of that content.
Can I still make a bootable copy of my startup disk with CCC?
Yes, although we don't recommend relying on External Boot as part of a backup strategy. See Creating legacy bootable backups of macOS for more information on how to configure CCC to make bootable copies of the startup disk.