Dda is the voiced member of the retroflex class, made at the same curled-back position as the letter that heads it with the vocal cords engaged. It differs from that letter by voicing alone, and it holds the third slot as the voiced stop does in each of the other four classes.
The letter is not frequent in classical Sanskrit, and much of its occurrence is in words of the same kinds that carry the other retroflex stops. Within a word, between vowels, the sound it writes had already begun to be pronounced in some varieties of Indo-Aryan as a flap rather than a stop, and the later scripts of northern India developed a way of marking that.
Siddham did not. The convention of writing a dot beneath the letter to mark the flap settled in India after Siddham had ceased to be written there, so the script carries the classical inventory and nothing that came afterwards. Reading a Siddham manuscript therefore means reading the sound system as the grammarians described it, without the distinctions that later Indian writing added for later stages of the languages.
That gives the script a particular value and a particular limitation. It is a good witness to what it was made for and a poor one for anything later, which is true of most scripts frozen by transmission into another culture.