The SW note is dumb, yeah. Seems you'd want to tie them together with a pour, for thermal capacity, but to connect nothing else (unless of course you want to try some snubbing or damping, which they'll never suggest, but that's where you'd do it).
The layout seems not inconsistent with the GND note; see that there's no other GND connections to the back side plane, so AGND is essentially tying to PGND at the point indicated. I don't see anything wrong with pouring copper over everything GND, top and bottom.
Tim