> If you accept a physical basis for fifths (by virtue of the harmonic series) then surely it's not a major leap (no pun intended) from that to thirds?
It’s not a leap to go from the fifth (as an interval, two notes) to the major triad, three notes. However, if you consider major triads, you’re just dipping your toe in the water as far as chords are considered.
The question is not, “Why does the major third above the root appear in chords?” but rather “Why do we build chords out of stacked thirds, which can be minor, major, or even diminished or augmented?” At this point, the part about the major third appearing in the harmonic series lacks explicatory power.
Consider, for example, that a chord “built out of thirds” can contain a major or minor seventh, a minor second, or an augmented fourth. Just as examples.