Someone on Reddit found the original stock footage that they used for that plane shot and they found that the original footage had normal windows which proves that the edits were definitely on purpose (especially since the footage didn't seem to be edited in any other way from the stock shot).
I'm sure Troy and the other guys were all big Lynch fans. It seems like a pretty obvious influence on them in the way that they structured their horror.
>I wish I could find the Ebert comments about MH
Here's his tweet about it: https://twitter.com/ebertchicago/status/5495205792
Ebert died before it ended so he'll never know how it was completed. It's the greatest tragedy of the modern era. (actually I'd bet he watched whatever was out at the time when he recommended it and then never watched it again)