Is a headerless table really supposed to have two \toprule with a \endfirsthead between them? It certainly is not the output I expected.

Please consider the attached files. The file 'consonants.txt' contains the markdown source for a headerless table, and a copy of the LaTeX source generated from that markdown source.
Note the two commented out lines in the LaTeX source: when they are not commented out the table gets two toprules, as can be seen in the PDF generated directly from the markdown file, where the second table, generated from the embedded LaTeX source with the two lines commented out, represents the desired output.

consonants.txt

table.pdf