It's one of his quirks. There's a few car design tropes that bug him and he'll complain every time he gets a car with them.
Personally, I like it, but hell as long as it's something that can be turned off then it's not a big deal either way.
Thanks for posting this, I'm considering a MKZ with that same roof and it's interesting to read about potential issues.
Glad it has mostly worked out for you, that repair timeframe is wild.