Theiler, whose plaque is on the motor, was a rather obsessive (in a good way) Ferrari service and tuner. Some opinions find this treatment attractive. After all, look how all of the newer Ferraris do this. 575, 599, 430, 360, 488, etc. I don't think they do it because it's ugly but because it looks good.
Why not? If you like it, you like it. It's only paint. Easy to strip off and set back to original with only a few hours of work.
Here's another way of looking at it. Prior to the injected Boxer the V12 cars did not have painted plenums because they did not have injection so they had no plenums. So as far as I know the Boxer was the first injected V12 Ferrari production road car. Every other production Ferrari that I know of after the Boxer had either red paint on their plenums or carbon fiber. So it would seem to me that after the first injected Ferrari V12 production Ferrari, and in fact after just a short run of cars overall, Ferrari decided it preferred its cars with Red painted Plenums. Ferrari switched to red as well on the V8 Cars starting with the QV and then the 328 and every V8 thereafter (except for the not so attractive plastic plenums of the 355 after the 355 every single V8 has red on its plenum.)
