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I am pretty sure the iOS Kobo app doesn't use any Adobe RMSDK code. After all, it is a dedicated ereader app for Kobo's books. And as Adobe isn't listed in the acknowledgements, it's pretty certain.
While I have read a little bit using the app, they have all been books I purchased from Kobo. But, I would be pretty stunned if epubs don't work. After all, a kepub looks like an epub with extra spans. They should pass any epub validation you can find. But, I have just tried a couple of epubs on my iPad. They are rendering correctly and the ToC navigation works properly.
The two that I tried that had a contents page worked, but had some problems. On one, the links for the chapters were all down the left side. If I wasn't careful where I tapped, it turned the page back. If I was careful, the footnote display was popped up and then let me go to the correct spot. The other book had the contents list centred in the page. Tapping seemed to be easier and the links took me the chapter correctly. Looking at the code, I would say the reasons for the popups is that some of the links are to an anchor in the chapter rather than to the file. The rest was probably my fat fingers. Increasing the font size meant I hit the links more often.
Now, I have a lot more knowledge about the kepub reader on the Kobo e-ink devices. If you are producing epubs that don't render well using the kepub reader, then you must be producing some very strange epubs. The kepub renderer uses ACCESS (which has been renamed) and is a popular alternative to using the RMSDK based reader. There are differences in how they render the books or exactly what styles they ignore, but the kepub reader does a good job of rendering epubs. And it has done so for a long time.
If you have books that don't work in either place, post them for others to look at. Or, pick a book we can all look at to try. Picking a book in the MobileRead library works well for this.
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