Please change the Retrieve apps call within the Deploy API to return all applications when a company admin executes the request. Currently the requesting user will only return a list of applications if they are invited to the project.
This perspective doesn't seem to take into account how Mendix partners work: we work for dozens of customers, and many times the projects are initiated by the Mendix partner instead of the customer. Should a company admin of a Mendix partner be able to get all these applications? I can't think of a customer who would accept that people who are not explicitly authorized for a project are able to get information about the project.
At one of our customers, we have a MendixMaintenance@thecustomer.com account. This account is invited to every project. API calls are done using the API key of that account.