Ok, you got me curious.  How does TeX know what application wrote the file
    if it's not "to do with" the contents of that file?

Sorry, I was referring to the one-line source file
\input texinfo @bye

As for the .fmt file, yes, it surely records whether tex, etex, pdfetex,
etc., was used to generate it.  Hence the error.

Ralf, what is the output if you run
  tex \\end
from the command line?  Also
  etex \\end
and
  pdfetex \\end

    This is e-TeXk, Version 3.141592-2.2 (Web2C 7.5.4)

This shows that texi2dvi is invoking etex.

    This is pdfeTeXk, Version 3.141592-1.21a-2.2 (Web2C 7.5.4) (INITEX)

This shows that mktexfmt is invoking pdfetex to build etex.fmt.

This mismatch is causing the error.

This is controlled by the file fmtutil.cnf.  What does that file look
like in your installation?

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