From what I've read about Clear Sky, it would make sense to me to have them perched up on top of the hill; as an organization dedicated to research, it would be the perfect place to observe the elements of the zone. From a tactical standpoint, it would make it harder for the free stalkers to assault from that direction (like we did so effectively last time) and it would also allow you to set Clear Sky up to do all kinds of different stuff, since we would have the high ground, so we would have a decent insert into pretty much any theater (the bank, Pripyat, etc.) the disadvantage being that we wouldn't have the element of stealth.
As for a building... It is true that there isn't anything up there, but we're pretty resourceful; I'm sure we can think up something workable =)