Can someone tell me why there is all this stuff in texi2dvi for
    processing LaTeX files?

A contributor (Akim Demaille) wrote the LaTeX support many years ago, on
the theory that the general process is identical.  I don't know how many
people actually use it, but I would be leery of removing it now, even
though it is definitely a significant complication.

    Possible problem: a *.fls file meets the *.??s glob pattern for sorted
    index files. Probably not a problem.

I have used, and still use, an "fl" index in actual documents.  So it
seems like it is in fact a conflict, unfortunately.  I doubt there is
any portable way to specify the recorder file name.  Sigh.  -k

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