Once you see it, you can never unsee it.
This is how it should be :
The meta seems less worst than the main site's. But the explanation is quite simple. It's the color used. If you take a look at this picture
You can see that the misalignment looks worst on the Main logo than on the Meta logo.
If you zoom the logos 1 and 2 and look at the second bar, you can see that the both bars have 3 pixels of shading around the main color.
The thing is the meta one is gray so the last shading pixel is light gray and is barely visible when zoomed out. Which is why you don't see the last pixels on the left and therefore, see it more centered.
On picture 2, the last pixels of shading is light brown which will still render correctly on a white background.
Take a look pictures 3 and 4. I simply took the Main site colors with the meta shading. Doesn't it look a little more centered ?
Still, thanks to you, my OCD will be killing me everytime I see the main site's logo. Please fix it.