I've got a black dial CSMP and the logo on mine is centered perfectly, and so is the pearl.
If your not happy with what the TD is trying to sell you for $318 keep asking for one you'll be happy with.
If I accepted a rep that I noticed had something misaligned in the QC photos, I'd see that every time I looked at it, and I don't care if anyone else would notice, I'd notice.
So keep asking for another till you're happy, or ask for a refund and try another TD, or wait for the next batch.
The CSMP on the website photo doesn't have a misaligned logo, so obviously the factory can get it right, and if they can't get it right on the one you're buying, the QC should be rejected. But don't worry, the TD's don't take the unacceptable watches back to the factory to have the defects repaired, they'll just sell it to someone who doesn't notice the problem.
I was surprised when I first started buying reps at how the TD's could not see obvious imperfections, damage, etc on the watches they send QC photos for, but I realized shortly after, that they can't be that stupid and unobservant, they just hope that their customer is.