I don't think they're quite explicit in mentioning auto ISO is available in manual, so that's probably why.
On the D7000 and up you get the second jog dial on the front of the grip so you have SS and aperture within reach instantly. Then there are various extra buttons that you press and hold, that then let you alter the setting - so if I hit the AF button, I can change between number of points with one wheel, and mode with the other. They're nice, but not that essential for me. The info menu on the D3100 is really well thought out, the SS/aperture toggle was right bu your index finger, my info menu was always on the AF mode anyway, and I had the ISO set to the Fn button (which incidentally is in a better place on the D3100 than D7000. You can fix that, but it ends up wasting an Fn button) :shrug:
I don't find I change anything else often enough to care.