Personally.. I'd let this particular case be story driven.. Don't charge benefit points (at least, not yet)..
Eventually, Lex is going to get free.. And he's gonna want his home back.. At that point, if anything, I'd make ownership of the tower a complication. Having one of the smartest, wealthiest and most ruthless men on the planet gunning for my head on a pike could very well be worth a hero point or so.
Additionally, as far as what that benefit would get you.. The old adage of 'you get what you pay for' fits the bill quite nicely. If you are going to use the tower as an excuse for players to spend points on new tech for their characters, make it cost 1-2 pts.. If they are going to get a ton of prestige for owning it, maybe another point. If they make some contacts, add points there too. It's all in what they are going to use it for, and how far you're going to let them take it... Don't charge them 2pts and let them walk out the front door with a rifle that could drop Superman, or fly out the roof with the super space ship that also travels through time and can make instant snow comes.. Just my thoughts.. The actual RAW rule is very loose.