I've had six mogs over twenty years three with and three without spare wheel covers, never noticed if the spare heel has deteriorated with the cover more than without.
Personally I would think that to get the best match to the upholstery/tonneau/roof material you'd need to get it done at the factory. However Sean at allon whites is an upholstery wizzard so if the car were a little older and an exact match were impossible then I'd plump for Sean to do the work. I think he'd be better value than the factory as well.