On this point I am going to defend MR. My thought process is thus:
Although words have defined meanings, many words have a range of meanings. More pointedly some words become invested with a personal slant that differs in some way, subtle or extreme, from the conventional meanings.
An example of the first sort, pertinent to this discussion, is the acronym UFO. To many people this equates to "alien spacecraft", to others it does indeed simply mean unidentified flying object. Some of you will recall the misunderstandings and arguments such a difference can generate.
I postulate that MR sees the word alien as relating specifically to entities from elsewhere in this universe and this time. In short, the conventional use of the word alien. I agree that time travelers, or beings from a parallel universe would fully fit the bill of one sense of the word alien. However, it does not follow that MR uses this meaning, or even perceives it to be reasonable.
Consequently, while his usage of alien may be confusing and frustrating, I do not believe it is conclusive evidence that he is - in this instance - displaying intellectual dishonesty.