Pointing out a plot hole isn't quite the same as authorial intent. Tolkien isn't saying, "I think that LOTR means X", he's simply, and quite rightly, pointing to a problem in the text. As an English professor, I would expect no less.
An arguement about authorial intent would lead us to the fact that Tolkien denied any allegorical meaning of the LOTR in reference to World War Two. Denied it vehemently. Despite that, there's a rather large amount of critical work that claims the exact opposite, that LOTR is allegory for WW2.
If we accept authorial intent, then all that work is meaningless. The meaning that those critics are taking from the text is wrong. Since that's a bit hard to defend, after all, they are flatly stating that that is exactly the meaning they are taking and are supporting their interpretations with textual examples, I'm not so sure that we can really rely on authorial intent.
So, really, it's not a contradiction since we're not really discussing intended meaning, but, actually fairly cut and dried plot elements.
For example, even if they couldn't fly straight into Mordor, howzabout instead of taking all that time hiking through Moria, they just fly to Lothlorian? If nothing else, they gain a whole whack of time.