People who are more likely to customize their app are more likely power users, therefore they're going to engage with the app more anyways.

Why would someone changing app colors to ones they specifically chose make them use the app less? There is no logic in that statement.

This sounds much like a post hoc justification for having not bothered to go to the effort to implement the ability to allow anyone (power users or otherwise) the freedom to customize the "app" to their liking.