Couple comments...
The wiki page mentions two HW tech for printing in Multiple colors
1) two or more motors & feed mechanisms feeding into one heated
barrel.
2) using an ink jet to color the plastic somewhere in the feed
mechanism
Both of these imply a single heated barrel and nozzle. The system
will have to calculate the proper amount of color to feed at the right
time, ahead of when the actual color printing will occur. (printing in
color 1 but feeding color 2 to get it to nozzle at the right time) It
will probably also have to account for some mixing of colors in
chamber - requiring some off-object noodling to clear the previous and
mixed colors. A nice multi-color object will probably not be
restricted to single color per layer, so there will be chamber
clearing each layer. I have heard (from Miles, aka TeamTeamUSA i
think), that sometimes a bit of color can get lodged in the barrel and
come out several minutes later. That does not bode well for chamber
clearing.
An alternative is to have multiple heaters and feeds. The nozzles
would need to be fairly close, and offsets inserted into control code
to account for differences in location.