The placements are supposed to be strategic, but sometimes the designers went with random instead. The sudden jut out of a hallway was meant to allow defenders a place to break line of sight and provide cover against intruders. It's particularly important when dealing with spellcasters, since it reduces their range (and makes fireball much more dangerous).Lastly, sometimes these modules have unusually shaped corridors and layouts for no good reason (in this case I think the reason is to keep sound from traveling too easy around the place, but that actually makes little sense given that it is a fortress mean to go on alert on a moment's notice). So, while I try to keep a little of the idiosyncratic shape, I also straighten a lot of it out. It is one thing if the map is of natural caverns being put to use as a lair, but a designed and engineered place presumably is designed towards its uses.
I totally agree on the room size for leaders, feeling that even a 20x20 is plenty. I also think your use of 3D is really, really good, since it makes sense for lizardfolk/sahuagin and can throw off players who think only in 2D.