Found the relevant pages for the other issues. Sorry if this is a dead horse already, but I thought it would be cool to review the quoted rules.
Page 6, under
Bases: "First, a model is considered to occupy the area of its base... For models without a base (usually vehicles) use the model's hull/main body instead."
Page 7, under
Model Height, 3rd sentence: "This does not mean literally their actual height, as the simple expedient of crouching, kneeling or crawling will render such direct comparisons irrelevant. Instead there are three broad height bands into which all models fall. These categories are also used to define the height of some [area] terrain features."
Sizes 1 - 3, as we know them.
Page 20, 2nd column, 1st bullet: "All vehicles, vehicle wrecks, monstrous creatures and artillery, friend or foe block LOS. LOS can still be drawn over or past such models, but not thru them."
So if page 6 says models occupy the area of it's base, (ie. dreadnaught, which has a base, level 3 model) under it's legs would be a space that's occupied by the model