It's all in the voicings though. The high D played on the bass means we're hearing the chord as a sub-dominant (the key of the song is G). Take the 12 string out of the equation and it's a straightforward Dsus4 chord. Without Harrison's guitar it wouldn't have mattered if Lennon's chord included the third (F#). Crucially it doesn't because the 12 string includes the octaved F natural.
I'd call it a combination of Gsus4 and Dsus4 both chords minus the thirds.

As regards how Harrison fingers it my guess is he fingers a normal four fingered F+9 but loops his thumb over to play the G and C on the bottom strings. Not impossible on the thin neck of a Rickenbacker 12