Applying the principle of "melody first," it's obvious that "Footprints" is a 12-bar blues in minor. If this were a generic blues, bars 9-10 might be harmonized in a way more or less like one of these:
| Dm7 | G7 |
| Dm7b5 | G7b9 |
| D7 | G7 |
| Ab7 | G7 |
| G7 | Fm7 |
The melody uses a repeated B natural (leading tone in C minor) in bar 9, to a long Bb note in bar 10. To my ear, that works best with either | D7 | G7 | or | G7 | Fm7 |. So here's hazarding another guess: Wayne wanted something hipper, taking one of these variations along a different route.
In the case of | D7 | G7 | , here's how it might have gone:
F#m7b5 is the same thing as D9, minus the root D.
It could then be recast as the II chord in a II V : | F#m7b5 B7 | . That's bar 9. In our "bio" progression, he drops the b5 on the F# chord.
In bar 10, triads on both E and A are perfectly good upper structures for G7. Also, using these chords allows the bass line to continue along the circle of fourths. The tensions indicated in the "bio," Sher, and Aebersold charts add color, yet don't do anything to spoil the overall "G7" function of the measure.
You might note that the old bootleg Real Book shows | D7 | Db7 | . In a reductionist sense, maybe the old RB wasn't entirely wrong, after all.
If the original route were via | G7 | Fm7 | , it might have gone this way:
In bar 9, prepare the G7 with a D7, substitute F#m7b5 for D7, then route it to B7 instead, as in the previous case; in bar 10, think Fm6 with E in the bass (this equals E7"alt"), then route it to A7, as above.
Also, I'm guessing that leaving the "7" off the B and A chords in the "bio" chart was inadvertent.
As for why the A7(#5, #9, #11) moves so nicely into the Cm9 that follows in bar 11, it's because 1) We totally expect a Cm9 there, and because 2) In Wayne's harmony, a dominant sound, creating tension, can pretty much resolve anywhere, into any tonic-sounding target chord.