There seems to be an issue with the way that material assignment is handled on geometry nodes level.
Right now the behaviour is quite inconsistent.
In some cases there is a default material assigned that is not assigned to any material slot of the object. That happens for both the pre-existing and generated geometry.
Muting and unmuting specific nodes has different effects on this. Especially muting the Group Input node (which should not even be possible and is not displayed in the UI) seems to reliably assign the default material, why muting and unmuting the Subdiv node, seems to reliably bring the assigned materials back.
Note that the material slots are selected so link the materials to Data and not Object.