But the granny flat does not officially exist, so I don't see any reason for the 3rd parking space there.
And it is said by the OP that he personally does not want the 3rd parking space, even though he seems to have 3 cars.
Was 3 parking spaces possibly specified by the planner, although only 2 are required by regulation?
Edit:
In the first post my suspicion is confirmed, the planner specified 3 spaces. What does the building permit say? For example, here the city reduced it from at least 2 to 1. If the textual part there states 2, you can do whatever you want. If that textual part does not exist, just ask the city....