Normally I think it is useful to ignore them in that case. Nevertheless you can (and I have done) explicitly added file names even if the directory name starts with a dot, such as ".fossil-settings/encoding-glob" and ".github/workflows/auto-assignment.yml".
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Fossil by default ignores files and directories starting with a dot.
So, even of you explicitly add a directory, any files or directories starting with a dot inside it gets skipped.
Normally I think it is useful to ignore them in that case. Nevertheless you can (and I have done) explicitly added file names even if the directory name starts with a dot, such as ".fossil-settings/encoding-glob" and ".github/workflows/auto-assignment.yml".
We do the same thing when specific files need to be added even though they are either dot files or within dot directories.