This bug, which continues to cripple HTML5 apps on the App Store but not ones accessed in Safari, seems almost too perfect to be unintentional.
I don't doubt that there is probably an explanation that makes sense, but based on what we know, the least malicious explanation is that they forgot to test WKWebView with local files, which doesn't make sense.
Honestly, with Apple sometimes I wonder. Safari had so, so many bugs when iOS7 launched that I no longer believe they spend a meaningful amount of time testing Safari before launch.