Further to the above, dont forget all this has already happened with High Sierra so Mojave is no different. See this article from Bombich June 2017;
Will CCC work with Apple's new filesystem, APFS?
"The current version of CCC 4 already works with APFS insofar as CCC can copy files to and from that filesystem. The current version can also make bootable backups from an APFS startup disk to an HFS+ formatted destination volume – we've already tested that, and in the little bit of testing that we've done so far, that works great. The current feature set of CCC 4 will be qualified against High Sierra – creating bootable HFS+-based backups and working with CoreStorage encrypted backups will be qualified and functional (barring any OS bugs) and we aim to complete that by the time Apple ships High Sierra in the Fall.
Creating a bootable APFS volume, however, is brand-new territory. The semantics of starting a Mac from an APFS volume are completely different from those of an HFS+ volume. We have established a procedure to create an APFS startup volume, though, and we've even created a proof-of-concept bootable APFS clone. What lies ahead is a massive amount of engineering work to build support for these new procedures into CCC. APFS encryption is also handled quite differently from CoreStorage encryption, so we have a lot of work to do in regard to building in support for automatically unlocking and mounting APFS encrypted backup volumes. We're aiming to offer new functionality for creating APFS bootable (and optionally encrypted) backups by the time Apple ships macOS High Sierra in the Fall."