The dependent sign for u hangs beneath the consonant, which puts it in competition for space with everything else written below the line. Subjoined consonants in a conjunct go there, the mark for the vocalic r goes there, and a syllable needing both a cluster and this vowel has to accommodate them in one stack. Siddham solves that as the Brahmic scripts generally do, by reshaping the mark or the cluster or both, so the u of a simple syllable and the u of a heavy conjunct may not look the same. A learner acquires the variants as part of learning the conjuncts rather than as part of learning the vowel.
In the vocabulary the sound is common and unremarkable, standing in a long list of ordinary roots and in several frequent endings. What gives the letter a place out of proportion to that is the old analysis of the syllable Om, which takes it to consist of a, u and m. The middle term is this vowel, and the combination of a with u is what the grammarians describe as yielding o, so the analysis is a claim about how sounds are formed before it is a claim about anything else.
The letter also carries an alternate form in the encoding of the script beside its standard one, one of the scribal variants a hand-copied tradition accumulates over a long enough life.