Dunno if i understood you correctly but here goes anyway...
I think you want to do a maze within a custom map that would allow some areas to be "harder" to move into by jamming ships path to a bottleneck center, right?
Indirectly, this could be achieved by using fake "invisible" ships -- but, it's quite complex.
First, you'd need a sort of neutral race which can't play and won't have a homeworld... but with the necessary amount of "ships". By dropping these elements on the tiles, everyone wouldn't be able to go through the tile without destroying the ship itself!
Thus, a hugely strong (like, maximum defense) invisible fleet deployed in the proper manner should work.
But, secondly... this way has an unforeseen side effect -- the fake race clugs the xml with it's special settings and thus, runs the risk of finding an enemy (be it an AI or you, btw) - eventually.
Instead of Dead Space... what you'd get is a set of tricky tiles represented by a bunch of invisible super-strong ships controlled by nobody. Sadly, just using the map features itself is not enough since the only true impassable tile is a star (or somehow, planets) and these can't be placed together close enough or freely on maps.
So, what you have is a huge mod to create rather than the easiest way -- a simple map which HAS a dead space tile feature.
My 2¢.