The dotted letters of the later northern scripts are worth understanding as a system, because they show how a fixed alphabet absorbs new sounds. Persian and Arabic vocabulary entered the northern Indian languages in quantity from the medieval period onward and brought sounds the inherited inventory had no letters for: a labiodental fricative, two velar fricatives, a uvular stop, a voiced sibilant. Rather than adding letters to the order, the scripts took the nearest existing sign and put a dot beneath it.
That solution has a specific virtue. The order of letters was a memorised object recited in a fixed sequence, and adding to it would have meant every reciter learning a longer list. A dotted variant is filed under its base letter, so the sequence is unchanged and the recitation still works. It is the same instinct that put the retroflex lateral at the end of the Brahmi consonants rather than among the laterals, and that put the three Tamil additions after everything else.
None of this belongs to Brahmi, and it is worth being clear about that, because a reader who knows a modern Indic alphabet may reasonably assume its refinements go back to the parent. The dotted letters, the explicit vowel canceller and most of the standardised conjunct forms are all later developments.