I have encountered the behaviour in QS QMC where a RootAdmin with an Analyzer token has LESS access than just a RootAdmin.
Having an Analyzer token will remove permissions that a normal RootAdmin has such as publish or delete of apps, and other abilities. Qlik has an article about this 000063467, but this idea suggestion is to change that behaviour.
Professional or Analyzer are a licence to view content in the Hub, and have should have no effect on QMC permissions. The QMC permissions are managed separately by the existing default Admin roles such as RootAdmin, and should be mutually exclusive from licences.
There can be situations where IT support need to manage the environment = RootAdmin + view the Qlik monitoring apps = Analyzer But having both will prevent you from accessing your full permissions.