At first, I thought the icon-inbox and icon-flag were positioned too high, so I compared to a beta site, and I determined that what is making them look like they're positioned too high is that the font color too closely matches the background color on the Workplace SE icons, which puts the eye on the rectangles instead of on the text values.
On the beta sites, the font foreground color is powerful enough to put focus on the actual text, which is centered between the top of the black bar and the bottom of the black bar.
When comparing the two sites, you can see the spacing is the same; it's just the colors drawing the eye to focus on different things.
As an aside, I like the orange color of the flag indicator background, just something might be amiss with the font-color. It would also be easier to read if the font colors stood out more. Hope this helps!
Actually, looking at the edit-count (suggested edit icon) the positioning does appear to be different. I don't think it matters since it's in a different group, but I thought I'd include another screenshot in the interests of being thorough.