Built within the last few weeks - I finally switched from the supplied pre-built dependencies to building my own from source too.
Actually, I haven't tested this since doing that...
...aha. Now I
do see the Ogre viewport toggle. It's a bit ugly as it rotates and stretches, then pops back afterwards, but it is working.
However my GUI stuff is still being messed up. Now this isn't Ogre's responsibility - you're off the hook

- but I still need to fix it. So I think I still need to catch some event and handle it, either an iOS event or an Ogre one. How is Ogre internally handling this - catching an orientation change notification and translating it to a window-resize action maybe? If you can tell me how Ogre is automatically handling orientation changes maybe I can dig through the code to see myself, but I'd still appreciate any higher-level advice.
Just for background, I'm using MyGUI for my GUI stuff as this is cross-compiling Win32 and iOS. I checked and on Win32 I can resize my window without this problem so either Ogre isn't treating them the same, or I have inadvertently coded different behaviour on my side.