In order to grasp how Schubert might have arrived at this unusual result, it's easiest to think in terms of improvisation while playing for dancing. The A Major Waltz bears a curious resemblance to a waltz in Opus 9 (D. 365): these are the only extant Schubert waltzes that open with a figure based on the supertonic harmony with a 7-6 suspension. As the graphic below shows, D365n6 (at the top) shares with the A Major Waltz not only the initial 7-6 suspension but also the subsequent 5-4 over the 6/4 initial component of a cadential dominant figure.
I discuss D365n6 briefly in the context of typical harmonic patterns here: "Description and Interpretation: Fred Lerdahl's Tonal Pitch Space and Linear Analysis," review-article, Music Analysis 25/1-2 (2006): 215. I will expand on the idea of improvisation as a source for D779n13 in tomorrow's post.
Postscript: Nicholas Cook offers a brief but trenchant account of the problem of parallel fifths in Schenkerian theory and practice. Writing about Schubert's song "Das Wandern," he concludes that a reading including middleground parallel fifths "is less satisfactory [than readings that remove the parallels] as an expression of that structure in terms of the metaphor of Fuxian counterpoint. [The fifths make] the music look ungrammatical and, therefore, incoherent. But this is not because the middleground consecutives contravene any natural law of musical organization. It is because they run counter to the representational means adopted in Schenkerian analysis. They spoil the comparison between Schubert's song and Fuxian counterpoint" (126, 128).
In that connection, here is a thoroughly "tamed" version of the waltz as a fourth-species exercise (with allowances for bass-specific leaps, of course).
Reference:
Cook, Nicholas. "Music Theory and 'Good Comparison': A Viennese Perspective." Journal of Music Theory 33/1 (1989): 117-41.
Cook, Nicholas. "Music Theory and 'Good Comparison': A Viennese Perspective." Journal of Music Theory 33/1 (1989): 117-41.
