I have a vague memory of seeing a picture of it from the old Mission to Zhodane (or whatever it’s called) book.
Iirc, yes, it docks vertically, and since the Rock is an asteroid ship the outer surface of the asteroid is some distance away from the inner ship parts, so the Pebble does fit within the asteroid, but not within the ‘ship’.
The Cargo and airlock hatches of the Pebble matches the cargo hold and upper deck docking space on the Rock, and the rest of Pebble extends above any below the two interior decks of the Rock.