`genindex` et al. inclusion in `toctree` directive results in a warning with the `latexpdf` builder

Describe the bug

Adding genindex (or any other special docname) works perfectly with the html builder, but, despite producing the expected output for the latexpdf builder, it always warns:

WARNING: toctree contains ref to nonexisting file 'genindex' [toc.not_readable]

Possibly an unrelated issue, I then tried this with no change, which means the only directive somehow works differently when it guards a toctree directive or maybe its block is still evaluated before being discarded.

.. only:: html
   .. toctree::
      :hidden:

      genindex

Either way I see no way of cleanly suppressing the warning, which is annoying since I wanted to compile with -W.

How to Reproduce

$ cat index.rst
.. toctree::

genindex
$ cat conf.py
$ sphinx-build -M html . html/ # this is fine
$ sphinx-build -M latexpdf . pdf/ # this is not fine

Environment Information

Platform:              linux; (Linux-6.15.6-arch1-1-x86_64-with-glibc2.41)
Python version:        3.13.5 (main, Jun 21 2025, 09:35:00) [GCC 15.1.1 20250425])
Python implementation: CPython
Sphinx version:        8.2.3
Docutils version:      0.21.2
Jinja2 version:        3.1.6
Pygments version:      2.19.2

Sphinx extensions

Additional context

No response

Reproduce the warning with the provided index.rst and the html and latexpdf builders, including the guarded toctree example. Trace how the latexpdf builder handles the special docname and toctree warning, then verify that the expected output remains unchanged and the warning is absent when building with -W.