For all the talk about mysticism, "Space Babies," "Boom," "Dot and Bubble," and "Rogue" were all pretty standard episodes with the typical sci-fi-ish trappings. Even the Sutekh story didn't really require extra story elements to work.
In the end, I think the "magic exists now" line is pretty overblown.
I thought that's what she was getting at at the time, though IIRC she didn't actually finish her sentence.