Beckett giving up fewer hits has absolutely nothing to do with anything. tRA doesn't care about how many hits a pitcher gives up, and that's the whole point of DIPS theory. The pitcher doesn't control how many balls in play against them are converted into outs. Lester has a .340 BABIP against him, when he's typically in the .290 range. What does that tell us?
More hits are falling in than usual. That doesn't mean that Lester's not as good as Beckett, just that more hits are falling in. That's something Lester doesn't have control over.
Beckett has a LD% of 22.4 as compared to Lester's 20.5. That means hitters are making harder contact against Beckett than they are with Lester. Lester's also striking out 4.3% more hitters faced than Beckett is, while maintaining a slightly lower walk rate.
You're complaining about a metric that has Jonathan Lester as being 0.1 Runs Above Average better than Josh Beckett. Talk about nitpicking.