Forgive me if this has already been addressed somewhere, but I couldn’t find it with some cursory searching of the forums and the suggestion list.

At some relatively recent point, the output panel began showing up white with black text, where it used to match the chosen theme. Because I use a dark theme (Cobalt), the output panel now looks pretty out of place.

Is there a way to fix this?

Yep. The solution is described here: https://forum.sublimetext.com/t/change-the-bg-color-of-the-build-panel-new-st2-build-2165/3799/1

Many thanks!