So what's the chord??

From the paper:

George Harrison on 12-string pairs 2 through 5: (A2 A3) (D3 D4) (G3 G4) (C4 C4)

George Martin on piano: D3 F3 D5 G5 E6

John Lennon on 6-string: C5

Paul McCartney on his Höfner bass: D3

Expert mixing masks the timbre of the piano amongst the guitars, leading to the "mystery."

Who's Paul Hofner?

Should read: Paul McCartney on a Hofner bass (semi-acoustic, violin-shaped electric bass guitar).

Fixed.