The goal is to keep the top bar consistent across all SE sites. It was hard to come up with one aesthetic that plays nice with all of our sites' styles. That's why we went with a very dark gray(it's not black!).
However, I don't want to be dogmatic about it. I believe there's wiggle room to tweak the top bar style slightly so it plays nice with a particular SE site. I've changed the translucency a bit on RPG.se and Scifi.se already.
For Ask Ubuntu, I agree the new top bar as of now doesn't look too nice next to the orange top nav section.
I pushed some tweaks to dev server. See the screenshots below. I made the top bar background color to have a hint of orange, I think it looks better with the orange section below.
new hover bgcolor:
Thanks to Takkat's suggestion I've updated the top bar bgcolor to Canonical's Dark aubergine. See screenshot below: