As a sailmaker myself, I'm going to chime in here....
I work extensively with clients that are quite some distance away, so I'm accustomed to working remotely. Had you ordered from my company, I would have asked what color the suncover should be and what side it should be installed on.
On my own Maramu, which had been retrofitted with a Nirvana electric furler in 1985, it really didn't matter what side I put the suncover on since I could select the direction of furling with the switch. I can understand if you have labels for furling and unfurling that you would want to retain the suncover on the same side.
I wouldn't have the sailmaker change the suncover at this point though. It will result in many extra holes in the sail. Perhaps he'll offer some financial recompense in exchange for you having to remember to move the switch in opposite direction.
Founder and President, Island Planet Sails LLC