If you ask for the formal answer, it is not so easy. When you finish your CfMD for Add-On, you have to make formal locked code. That mean, you cannot made customization in selling process.
But, when you are in implementation process, you can make some customization on the same way, as you make them on standard NAV code, according client requirement.
When you register CfMD, you have right to register 10% objects more that you are used in development.
Everything is related with requirements and your possibilities, and of course your and customer license.