"Yes!" She doesn't even seem to have to think about the answer - maybe since she already did the thinking a moment ago. Considering what she already said just now, she's not going back on it. So Madoka just keeps smiling at him, even now as he comes on a similar level as her.

If anything, it's just sweet of him to ask if it's really alright. It shows the care Ignis always puts into everything. Maybe some people would say he's kind of holding himself back with being so careful, Madoka just thinks it's really nice.

"Mis.." She starts, but then quickly shuts her mouth again as she seems to realise something. ".. Ah, it's probably a little weird for me to still call you mister Ignis then, right..? It's a little formal.."

Granted, she was the one who insisted on saying mister to begin with, but she was just trying to be polite back then! And that was far, far beyond she ever even considered the possibility of him seeing her as a daughter.