data-* attributes on all the elements. But switched up and randomised so you wouldn't be able to strip them out with a single line of XSLT; and for greater annoyance, some of them would be required to make the design work, so stripping them out with a regex would break things.
Make 'em work for the free html they designed with your tool...
If it seems like a waste of effort on both sides, that's because it is.
Given that tools like this appear to be easy to write and easy to launch they should probably be sold to hosting companies not designers. As in, you'd make more money selling AutoMattic the whole shebang to use for designing things on top of Wordpress or it's successor than you would trying to sell $9/month subscriptions to would be web designers.