I cannot reproduce any problem with the viewport on an iPad Air 2 with iOS 9.2.1, nor a Nexus 9 with Android 6. I did however find one issue on the iPad, which was a similar thing to what you described: it seemed to zoom in on the top-left area after putting the device to sleep and waking it again. I found a horrible hack to work around this, and would report this issue to Apple, but bugs.webkit.org isn't responding right now
We don't have an iPad Pro in the office to test with right now. I don't know if the issue I found was related, or if this is an issue limited to just the iPad Pro device (which would be weird). Anyway wait until the next beta comes out and let me know if it's any better.