Well yeah, of course time stop from a non-magical source would affect them, because their resistance is due to Magic Resistance in the first place, like you said before.
Except in the Nasuverse, Magecraft is just a catch-all term(Curses, Alchemy, Kabbalah and even shit like Breathing Techniques are Magecraft or damn close to it to still count) and Magic Resistance, despite it's name, doesn't cover just Magic...
Magic Resistance (対魔力, Tai-Maryoku?, localized as "Anti-Magic"EX) grants protection against magical effects. Differing from the Resistance effect that merely rejects Magical Energy, this ability cancels the spells altogether. Magic Resistance is the Class Skill of the Saber, Lancer, Rider, Archer, Ruler, Shielder, MoonCancer, and Watcher classes.
This is why Type-Rey basically left out of here, you act like you know more than you actually do.