From what I understand, Media 100s hardware works in YUV, and the incoming files get stored as YUV files (e.g. in the Media 100 i codec). If these YUV files are accessed via QuickTime, like in AE or QuickTime player, they are converted into RGBA. All processing in AE happens in RGB colorspace before the files get written back into the Media 100 i (YUV) codec.
Some older hardware (including the first AVID systems with the pre-Meridien boards) worked in RGB, which made a conversion from the incoming YUV signals to RGB and back to YUV for output necessary. Most of todays hardware is YUV, though.