Google does seem to assume that their AdWords API is used primarily for in-house reporting and account management (as well by advertising agencies managing accounts on behalf of their clients).
Even if you are building an app for general, public use, the app's Client ID, Client Secret, and Developer Token are still connected to your company's MCC account.
However, this does not cause a problem. Any AdWords account owner can authorize your app to access their data, without having to be your client.