I guess that could indeed count as an "external TOC", but I've never personally come across a MobiPocket book that didn't have a hyperlink to the TOC within the book itself - have you? I agree that one could create such a book, but why would you? Does every device which supports Mobi support Guide items? If not, and you did your TOC that way, you'd have no way to get to it.
The original question was about whether it's a good idea to have a TOC that's in a separate file. I don't think that it really matters whether or not it is, but I can think of absolutely no good reason whatsoever not to have it available within the book, regardless of whether it's a separate file during the build process.
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