"No true Scotsman" is only a fallacy when one uses irrelevant criteria to exclude people from a group.

It's not NtS to point out that James "Scotty" Doohan wasn't Scottish (he was a Canadian of Irish descent.) Nor is it NtS to point out that certain people don't hold various relevant defining characteristics and therefore to claim that they don't count as being in a particular category. Of course, that exclusion is contextual -- it can apply to a particular use of a label without applying to all uses of it.

Note that I disagree with Sam Harris overall. His claim is that the only way Muslims can be reasonably said to exist is his definition; I would argue that one way Muslims can be said to exist is his definition. I would further argue that some people who use other definitions of Islam have irrational/unjustified/disproportionate fear, and can therefore be said to be Islamophobic.