A writing system for Sanskrit has to separate the retroflex consonants from the dental ones, because the language does. Words differ by nothing else, and the difference reaches into the grammar: a rule converts a dental nasal to a retroflex one under stated conditions, and another does the same for the dental sibilant, so the two series are not merely two sets of sounds but two states that the same sound moves between.
Every Brahmic script accordingly carries both series in full, five letters each, and Siddham is no exception. That is one of the design requirements that distinguishes this family of scripts from the alphabets of the Mediterranean, which have one t and one d because the languages they were built for had no reason to want more.
The consequence for anyone reading Sanskrit outside its own script is severe. Latin transliteration marks the retroflex series with a dot under the letter, and where the dots are dropped, which outside specialist publishing they usually are, the two series collapse into one. Words that are distinct in the language become identical on the page, and a reader has no way of telling which was meant.
The atlas records the distinction on the letters themselves for exactly that reason. The plain spellings used for readability cannot carry it, and the letter pages are where it is kept.