I take back what I said about the margin bug being fixed.
It turns out that in iOS, even if you delete a book entirely from within Kobo, if you then re-add the same book without explicitly killing Kobo in the task switcher, you'll find yourself looking at the old copy of the book. This fooled me into thinking that the bug was fixed, when in fact I was actually looking at a newer copy where I had worked around the bug.
So if you want compatibility with Kobo for iOS, do not under any circumstances set the left and right margins on the body tag to zero.