Thanks for looking into it, Dan.
I played with it more over the weekend, and it seems related to the image dimensions. PNGs above a certain size kept their transparency (seems to be either width or height)–but once I cropped below that, iOS automagically flattened the transparent pixels to white. Of course, the kind of things I wanted to use in MD2 were below that magical size.
In any case, Files integration would be great—I’d love to just browse to / drop in images (or layouts, or pages) instead of putting them in my (magically destructive) camera roll. It would also be a handy way to manipulate layouts without email or Dropbox.