Made some further tests. Seems that AECO does an automatic change to the first subtask when opening a specific task. If you set the root task to autoload (in ...taskNavigation.xml inside the prefs dir) then you wont even get the root, but the first available subtask.
Seems that currently there is indeed only the chance to make changes to the delivered dgnlib and load the changed one from a network place.
IMHO this should be subject of change as it prevents admins from using common customizations for both AECO and pure MicroStation and 3rd party developers from delivering their tools in a way that Bentley propagates (using dgnlibs)