Dave Nanian, developer at Shirt Pocket:

This means that, for those using El Capitan, we can’t hint obliquely that we’re compatible, as we have in the past, where our current version worked even though we couldn’t declare that compatibility until the final build. This time, the current version of SuperDuper is dead in the water on El Capitan. It just won’t work.

But don’t dismay: we’ve worked to change that. I’m happy to say, to those of you who are on the Beta (and those who are going to join the public beta today), we’ve developed and tested a Beta version of SuperDuper that makes bootable copies of El Capitan.

It’s a clever workaround that only requires the user to reinstall the OS from the App Store after booting from a backup. This means you’ll have an extra step before becoming fully functional, but without that additional step you’re vulnerable to certain types of malware (although, I’m not aware of this kind of malware existing in the wild). And as an added benefit, the OS reinstall builds certain caches which will speed up boot time.