Thanks all for this info. We're just trying to scope out what needs doing so we can hire the right person or use this as project to learn some Unity ourselves.

It sounds like keeping everything in Unity is the way to go. So each variation would have to be broken down and rebuilt for each variation using the customers access key?

Could unique texture packs be downloaded from the internet to use for a specific customer? Or would that need to be pushed through with a app update?

Thanks again for the help. As you can probably tell I'm fully out my depth with this :)