During the installation, the installer takes certain assumptions on the way how a kit created for an installed Qt version should work. Currently, in 2.0, the installer creates a kit called "Automotive 5.9.4 Intel NUC" which is preset to work ONLY with boot2Qt devices, and this cannot be changed for some reasons.
The recent Qt Creator plugin APIs have been changed in such a way that a plugin for Qt Application Manager does not need to be based on Boot2Qt. This current implementation of the Qt Application Manager plugin for Qt Creator requires a "Generic Linux Device" type. Due to this, the auto-created and auto-detected kit cannot be used with a device using Qt Application Manager.
The above makes the default setup made by the installer not usable and requires the user to create a new kit manually. This fact is not documented either.