The long vocalic l is the one letter of the syllabary that writes nothing. No attested Sanskrit word contains the sound, and the letter exists because the arrangement demands a long partner for every short vowel, not because anyone ever needed to write it. Saying that plainly is more useful than explaining it away, because it shows what kind of object the table is.
Everything follows from that. The letter is drawn in the charts, recited in its place, taught to learners of shittan in Japan and given a character of its own in the modern encoding of the script, on exactly the same footing as letters that appear on every page. A tradition transmitting a syllabary is transmitting a description of speech, and the parts of the description that happen to be unoccupied are still part of it. Dropping them would leave a shorter list and a different claim.
It also explains a discrepancy anyone comparing reference works will meet. Counts of the Siddham letters differ according to what is being counted: the letters of the traditional order, the letters plus the vowel marks and the cancelling stroke, or the characters an encoding needs to represent a manuscript, which include scribal alternates and marks that are not letters. None of those counts is wrong and they are not interchangeable. This atlas holds the forty-seven of the traditional order.