Geever was making a different point, one that is overlooked in most feature requests (and there have been several lately). You want this feature (ability to build on all squares) because it will make the game easier for you. But that doesn't make the game more fun. It just makes it easier.
Players usually want things that will help them win -- better weapons, more base space, larger squads, etc -- but the fun of the game comes from overcoming challenges. Good game mechanics typically involve simple problems with more than one way to solve them. That's why the blocked squares are there. Every base is a new challenge. Since replayability is key for us, the constant variation is important.
Don't get me wrong, challenge is important to me. I don't cheat lightly or indiscriminately - things like infinite money or hacking my soldiers' stats to something ridiculous doesn't appeal to me. But I do like to get the most out of what the game lets me do. To me, reloading my game a bunch of times to get a different base layout isn't really any different from picking the best soldiers out of the recruit list to make up my team.
But in this case, having the freedom to build my base how I want is more important to me than the extra challenge of making do with less space. I would mind the blocky squares much less if there was a base building that is just a regular square which you could build on top of them, letting you spend some time and money to get rid of them. I mind having the total square limit for my new base decreased for no good reason much more than I'd mind, say, getting 3-5 unbuildable squares in each base and having to pay 50,000 and spend 1-2 weeks clearing those spaces, though the economic cost of the latter may actually be higher than what the squares are worth in terms of gameplay benefit.
I don't mind variation, either. I'm taking care to build each base differently this time, with the entrance in a different location, so I don't have to replay the same base assault a dozen times over. But (for me at least,) it's an effort vs. reward thing. Having more space to build is literally priceless, so I'm willing to go to quite a bit of effort to secure that space. On the other hand, it's not likely I'm going to replay a mission because I'm not satisfied with the number of plasma pistol drops.
Random variation, IMO, is best used in places where the difference it makes is minor enough that it's not worth trying to force a specific outcome, or where other factors complicate things so the player is forced to compromise. The blocked squares, on the other hand, seem like a lazy mechanic to me, a cheap way to add more difficulty, but no real complexity. Fake Difficulty, to use tvtropes lingo. I'd rather find my challenge elsewhere.
