Congrats, you've figured out the concept of normalization.
Look at the "+" stats for normalized numbers. The normalized numbers show how well the pitcher did compared to the league average. 100 = league average. Higher is always "better".
That said... normalization for HR's is not done nearly as well as it should be. For some reason, the raw number seems to matter a lot more then the normalized number does when it comes to HR's by pitchers.Now, by the same token, I believe you will find Joss giving up (a lot) more 2B and 3B...