grey,
You may be correct that I am misunderstanding you. Here's some information that may clarify the issue.
If you are shooting with a 6D, then the full sensor is 5472 x 3648 (not 1824x***). Of course, when you are shooting video, the frame size is smaller, either because it is re-sized (normal mode) or because the sensor is being cropped (crop mode).
If you shoot raw or mlv and push the zoom button once, that puts you into (magic lantern) raw crop mode. In this mode you can shoot at higher frame sizes than in normal (non-crop) raw mode. This is because there is no down-rezzing taking place in crop mode; the sensor pixels are read one-to-one from a reduced (cropped) area. When shooting in crop mode, the actual framing will not match what you see on the LCD screen. You can use grayscale preview to see the correct framing, but if you use it while you are recording then it may cause issues such as "tearing."
If I am still misunderstanding your question, please re-state it in another way.