Ha! At first I was going to post something snarky like "the icons are aligned, they're just not aligned the way you expect them to be."
I assumed that a little photoshop measuring would show that even though the main icons don't line up directly with the dock icons, they would at least be centered as a group, over the dock icons. In fact they are not.
The guides here show that there is more space on the right side between the edges of the last icon in the dock/the edges of the last row above the dock, than there is on the left side.
So not only are the main icons not vertically aligned to the dock's icons, they're arbitrarily aligned horizontally.
Good job UI team!