The same way Grey does not match many sites either, including the original XF design. The idea is to have a standard product that matches the theme, no? As you said very well, users can customize the colors after. IMO, the editor color sticks like a sore thumb around the blueish theme XF has. For example the bar background should have a standard color present in XF scheme, so it changes automatically when the user modifies the global variable.
I disliked the greyish look of TinyMCE myself, but the default styling of redactor is too greyish for my taste. It suits greyish forums but not so much forums that use white, blue and orange, just like xenforo's default theme.
It's using style properties, which aren't defaulting to primaryLight and what not. At this point, it's still consistency. They haven't made sweeping changes to the style between 1.x releases, so styles will still function.
Such a massive change to the editor will force customers to make changes, which isn't and shouldn't be the goal.