Yep, that's it. In the original it was used briefly to command the ship in the battle of Pluto when they sunk and got the ship upside down. If you go to starblazers.com i think theres one of the few layout designs for the thing, basically it had the control room mirrored on the ceiling so that when the ship was upside down they used the consoles that were there and when upright the ones on the floor. Guess gravity control was discarded for the sake of something they thought would be cool. Guess it tanked since they never used it again in that fashion. Other than that, as far as i can remember, they only used it in the same way they used it so far in 2199, as an access port for personnel and machinery.
One of the reasons i've read in an interview with Leiji Matsumoto for the existence of such a structure in such a place was that the bottom of the ship just looked too flat and empty compared to the upper part so they went with it just to add some interest. Personally i like the look though i do laugh a lot to myself every time they land the ship in solid ground. XD
As for the holes on the bow i think they were just a stylistic modification of the real Yamato's bow. If you look at it, it had two openings on each side while the forward one was not a hole but a crest, 6ft in diameter, used only on very important imperial navy ships (More info here
http://www.battleshipyamato.info/characteristics.html) Besides, it looks cool
