Quick answer: Just for "clarity". Root being the lowest is "standard" on guitar playing
Long answer: As many other fellow guitarists pointed you out, there's a lot of ways to play the same chord. In this specific scenario we are facing, A is a note on this D chord, so, it can be played and it won't cause any trouble. But, bear in mind that most of the time, humans feel like the lowest note is the root. That's why (most of the time) bass players are playing around the root and reinforcing it through the piece. Bearing that in mind, the same chord can take multiple names. For instance an A D F# chord, could be an F#m( with the augmented 5th) (F# Root, A minor 3rd and D augmented 5th). So depending on the "inversion" (or the way you order the notes) you can get an F# based-chord or a D chord. The same may apply to any other note on the chord (or even notes that are missing, but that's another thing). As this example, there's no A chord that would drive your ear to A-land, as D is the 4th of A and F# the major 6th, so this chord is not "strong" in a functional sense. As I said before, bass plays and important role here. If you play this chord and the bass plays an F#, that would drive your ear to the F# as the root. If, for instance the bass play a D that would drive it to the D.
So, playing an A in this particular spot I don't think can make much difference (D is way more "powerful" than an augmented chord, because of its stability), but notice how changing the order in which you play the notes on a chord (by order I mean in a highest-lowest scale) can drive the listener to believe it is on one tone or another. No one has the right answer in which tone would an A D F# chord played without further context, meaning that the same chords can serve different purposes depending on the composition.
But, as I already said, generally we tend to think that the lowest note is the root, and therefore that the chord we hear is in the tonality of the root. Of course there are many other factors that come in play here (inner tensions, chord progression, idiomatism...), but as a rule of thumb that will do it. That's why, probably they muted the A note.
Possibly it has other reasons too (you are already playing an A on your 3rd string and you don't want to play two notes an octave apart if this is not the root note for the same reasons I already explained), maybe simlpicity can be one of them (I like to play a G open chord with my ring finger on the 3rd fret 2nd string, although many people would leave that ring open), not confusing people...
Hope this helps out!