This is what I'm seeing:
In Mercury during playback the Now Marker is a small, dark green triangle on a dark gray background (it's a little hard to distinguish the green color, actually).
In Tungsten, it's a larger black triangle on a lighter gray background.
Given the way themes use image files for graphics, I would not have expected the Now marker colors to be customizable via Colors in Preferences in any theme other than Mercury, which isn't technically a 'theme' in the same way that Tungsten is.