My small camera bag has 3 slots. I put a second lens in the left slot, the lens hoods for two lenses in the right slot and the camera, lens down in the centre slot. The camera would not fit in lens up. The flaps on the top of the dividends protect the front of the camera from the top of the lens and hoods. The slot is deeper than the length of the lens so the front element is not being rubbed against the bottom of the bag if the lens cap comes off. The camera is much quicker to get out and put away than it if was body down.
My large camera bag works in a similar manner, but if I have a longer lens such as a 70-200 or 50-500 on the camera it will lie flat on the top, above the other lenses, hoods, Flashtrax, patch cords, etc. I just have to turn the tripod mount to the side so the top of the bag will close.
In the camera back pack, I ususally have a telephoto lens mounted on the camera and it fits in flat. There are supports for the camera so it hangs lens down when I zipper the pack shut and hang it from my shoulders.