The independent letter A is written only where a word opens on the vowel, and in the Buddhist vocabulary copied in Siddham that turns out to be very often. Sanskrit forms its commonest negative by prefixing a short a to a word, or an before a vowel, and the doctrinal terms built that way are among the most repeated in the whole literature: the word for impermanence, the word for no-self, the word for non-violence. A page of doctrinal argument therefore carries the independent vowel far more often than a page of narrative would, which is one of the small ways the subject of a text shows in its letters before anyone has read it.
Elsewhere the letter is invisible in the ordinary sense, because it is the vowel every consonant sign already carries. A reader meets it as the absence of any other mark. Where a consonant closes a syllable with no vowel at all, a stroke is added to cancel the inherent a; where two vowels meet across a word boundary, Sanskrit merges them by rule, so a short a followed by another short a is written as the long vowel and the join disappears from the page. Reading Siddham means undoing those joins, which is one reason the study of the script in East Asia was never separable from the study of the grammar behind it.
In the teaching of the table A is the first thing said and the first thing written. Its position is not an accident of arrangement: the phoneticians put the least shaped sound first and worked outwards from it, so the letter that opens the syllabary is the one that asks the least of the mouth.