I, too, very soon found that creatures have a stupidly large amount of trouble navigating over buildings. The solution I have found works quite well (but only on the planet's surface) is to use "plaza" areas from the terraform tab to create a seemingly non-dirt ground area, my favorite being Tech Plaza. I found this to be the only way to have my NPC Runlar character move even close to where he was supposed to go in my nearly-complete "Base Command" adventure, since he had to take a turn. While using buildings for the floor, he would often move about 3/4 of the way to the turn in the corridor, stop for a moment, then turn and walk straight into the wall.
for information about path finding and buildings.
Short answer -- NPC walk around buildings but over disguised gates, but won't walk over disguised gates if they won't walk over what is under the disguised gate.