I think it was intended to prevent the dominance of a single, optimal base layout. The player must always adjust his plans.
If so, it seems like a solution in search of a problem—the game already punishes trying to conduct both research and production in the same base, making specialization obligatory (and thus requiring at least two layouts, probably three if you count the initial base where specialization is impractical without demolishing a bunch of stuff later). More to the point, at least in the game as it stands layout simply isn't very important—Large Hangers, Living Quarters, and the Command Center go clustered near the entrance to keep entry points and soldier spawn locations close, the power plant goes on the far side of the spawn points from the entry point (since it needs to be built quickly to activate the base), and antimatter goes on the other side of the map. Beyond that it's just a matter of ensuring space for the two-tile facilities and making sure you can build an advanced radar before scrapping your standard radar.
IMO, the possibility of more than one blocked square serves no role other than a source of irritation, and I wouldn't be too sad to see that last square go away, either.
A lot of the pain points I have with UFO:AI's design have to do with finding the line between creating potentially interesting obstacles (blocked squares, soldier death, bad-quality recruits, etc.) and simply encouraging savescumming. I think this issue is clearly on the savescumming side of that line, and apparently so do the previous two posters.
(This analysis may change if multilevel or otherwise larger bases become possible.)
~J
