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Cannot find master file when only_build_toc_files is enabled

See original GitHub issue

Describe the bug

I’d like to use the new only_build_toc_files setting which looks like a good feature, however it is not working as I expected.

To Reproduce

My original _config.yml file looks like

exclude_patterns: [
    # a bunch of glob patterns here
]
only_build_toc_files: false # TODO: enable this setting 

execute:
    execute_notebooks: off

sphinx:
    config:
        suppress_warnings: misc.highlighting_failure
        mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

When I change only_build_toc_files to true I get an error sphinx.errors.SphinxError: master file /Users/paddy/git_repos/course_mlbd/index.md not found but that file index.md is there and is in my _toc.yml as - file: index.md.

Expected behavior

My understanding is this new config just determines what is built which should be only the file specified in _toc.yml. Just to check that to stop executing a notebook it would still need to be in exclude_patterns?

Environment