Branded Site Links

My company sets up application websites for customers on its own domain which live in a folder. We’re now offering a private domain option so that the customer can run our software from the convenience of their own domain.

In our current setup, we have footer links at the bottom of these websites pointing to our marketing product pages. For these private domains, they will now be technically external links pointing to the same product pages.

The purpose of the CNAME is legitimate, but will these links now be considered Gray/Black hat?

I don’t see there would be a problem with those links – they are perfectly legitimate links to the site creator, which is just like a form of advertising. There’s nothing dodgy or unethical going on there, the links are exactly what they look like. It’s very common for site developers to link back to their own site in the footers of customers’ sites.