You don't need to do anything
If I get an article customized (physical, virtual, software, etc), I don't expect to know which features were customized for me. By adding these customization, I know the whole item has changed and it's unique for me. Adding a notice about differences will make me expect different behaviors or wonder about differences with other clients' setups: Is mine better? Is mine worse? What does other clients (or even worse, my competition) share in common, and what do they have that is better than mine? . In short: they will create friction on something that is not needed at all.
Additionally, the knowledge of something being added up on top of existing software usually sounds as a patch or bug fix. I mean... if you could do it right now, why didn't you start with the right version? Why isn't this software having the features that you tell me are better for me? Is this just a gimmick to charge me more?
As you can see, explaining customization is a double-edged sword, and has more issues than benefits. So just focus on providing a clear interface and proper controls and forget about letting your clients know something is different, even if they know. The last thing you'll want is to have your clients think too much on your product or service.
Finally, if your marketing people tells you they want to do something special, simple white label your software and that's it: you won't worry your users and they'll still see their brand in your software.