The independent long a is needed only at the head of a word, and in Sanskrit that position is filled more often by rule than by the shape of any root. A short a ending one word and meeting a short or long a beginning the next merge into a single long vowel, so a great many long a sounds on a page are the seam between two words rather than a feature of either. Written in Siddham the seam is invisible: what stands there is one letter, and separating it back into its parts is a judgement the reader makes from the grammar.
After a consonant the length is not a letter at all but an added stroke, and the economy is worth stating plainly, because it is the whole design of an abugida. Forty-seven letters and a small set of marks generate every syllable of the language. A reader who knows the consonant and knows the mark knows the syllable, and no separate character is needed for the hundreds of combinations that result.
The letter carries a further weight from the shape of the vocabulary. Sanskrit forms most of its feminine nouns and adjectives with a final long a, so the goddess names, a great many abstract nouns and a long list of doctrinal terms of feminine gender all close on this vowel. A page of devotional or philosophical text written in Siddham ends a high proportion of its words with the stroke this letter stands for, and a scribe who confused it with the short vowel would be changing the gender of what was written, not merely its length.