While I'm happy that you're getting into the premium theme development, I am not really agreeing with what you're trying to do in this regard. The first concern is the fact that your product is a theme, and ours would be a plugin. They're not mutually exclusive, and I can't think of any way to tie them together other than you providing our code with the zip file. Would you be setting sites up for these people as well, so that CPTUI gets used for it?
The second concern is if they'd end up getting updates to CPT UI from yourself, or if it could be handled by the native plugin update mechanism in WordPress through the .org repos. I'd definitely prefer that they get the updates straight from us, in the grand scheme of things.
A third concern would be what would stop them from removing the plugin for something else, or editing the theme's functions file to add their own CPTs without plugin? Once the code is out of your hands, you can't control what a user does with it.