I consider this a feature, not a bug. No matter what your device is set to, you can control how you read in Moon+. I think I remember that when the Nexus 7 or maybe it was another device first came out, you couldn't set it to auto rotate. If you used Moon+ you wouldn't have to worry about it.
I always have my device and reader set to auto rotate, but there is an occasional comic that is landscape but you need to turn your device to portrait to look at it properly. I just set Moon+ to a non sensor setting and it won't move when I turn the device and no other app is affected.
I was confused when the OP talked about having to set the rotate in two different places - set your device to whatever you want for most apps and leave it alone, and set what you want when you read in Moon+. The device setting never needs to be changed for Moon+, use Moon+ only for your reading setting.
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