One of the funniest bits of Stormblood was when the party splits up to look for something or other, and when you meet up with Lyse again, she's just hanging around the wreckage of at least one Magitek armour surrounding her. She doesn't even mention them; encountering and breaking Imperial Magitek Armour is just something to do in passing.
I figure M'naago was assuming that we were at least on par with Lyse, and so of course we wouldn't be bothered by any type of Magitek armour.
