He's not sure why this is such a thing, but Ignis really isn't trying to make her nervous or upset. He's far more upset she's even being included in this battle when she shouldn't be. So as he stands there trying to come up with some sort of compromise Madoka pipes up.

"If that's more comfortable for you, that's fine."

The advisor can understand formal and polite because he does it to the others back home so he definitely relates. And he'll go out of his way to make sure his team is alright, especially if small things like this will help them somehow.