I so rarely use the landscape layout that I have it disabled. But, checking now, I see the same thing with epubs. I think you are going to have to accept this as a "feature". It is probably happening because of the way the Adobe RMSDK works and the interaction with UI. The Adobe RMSDK is what is used for rendering epubs and there are lots of interesting things with how it works.
You should report it as an issue to Kobo. It is possible they can fix it, but, they need to know people care about it before they are likely to spend time on it.
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