Try a different MOT station.
Ground clearance can`t be an issue as the car was homolgated like it is.
I have similar discussions with the ecomobile nearly each time. Till now I won them all.
Best one is that the test engineers have to do a test drive with motorbikes and the eco is registered as one.
With the eco the simply can`t;-)
And it is written in the homologation papers that driving on public roads is only allowed after special training.
MOT engineers do not like this part...
Ground clearance becomes a problem when you find out the car you just purchased does not comply and is not as supposedly "homologated"