It is clear that having a session level in the hierarchy is optional, but it is unclear to me whether it is optional in file names when a session folder is present. For example, is this valid? /sub-01/ses-01/anat/sub-01_T1w.nii.gz

I would recommend clarifying this sentence under File name structure:

For a data file that was collected in a given session from a given subject, the file name will begin with the string sub-<label>_ses-<label>.

Cheers