Why is CheckBlock called twice when processing a new block?
I suspect this is an artifact of the way the code used to work. As to why it hasn't been taken out, it's probably just out of caution, or a "Don't fix it if it's not broken" mindset. Bitcoin Core coders are very cautious, and reasonably so since it's a piece of software that is the main interface to the network for many big players in the industry.

In addition, on master right now, CheckBlock contains a check at the beginning to avoid doing the same work twice. (Added in this commit.)

if (block.fChecked)
    return true;