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Per [man gitignore](https://git-scm.com/docs/gitignore) there are four sources of patterns for ignoring files. Command-line arguments are probably too much hassle; `.gitignore` is itself version-controlled (unless you include `.gitignore` in it), which creates complications. That leaves `$GIT_DIR/info/exclude` and the file listed in config variable `core.excludesFile`. Sadly, it seems that `$GIT_DIR/info/exclude` has to be a file and not a directory whose contents are concatenated.

A somewhat complicated solution which probably doesn't conflict directly with anything you're already doing would be:

1. Create a script which updates `$GIT_DIR/info/exclude` to list the .pdf files for which there are .tex files. If you want to be really cautious you could delimit a section of the file with comments and replace only that section.
2. [`alias`](https://ss64.com/bash/alias.html) `git` to invoke the script and then pass the arguments along to `/usr/bin/git`. (In practice this probably means making the script itself pass the arguments along, and make the script the alias).