Does the second channel of a C2 image represent the alpha channel or do they just fill the gap between C1-C3,C4?
You are mistaking colorspaces with channels. For example you have a greyscale colorspace, which is represented with 1 channel. Then you have BGR with 3 channels, and BGRA with 4. Here the 4th channel is the Alpha value. OpenCV supports several types of colorspaces.
OpenCV is opened to your needs, in some cases you have a mat with 2 values per pixel, for example Dense Optical Flow results, which have a vector of movement of each pixel (x,y vector). You may even create a greyscale image with alpha value for whatever reason or algorithm you have... in this case it will be a CV_8UC2. However this is not a standard colorspace in OpenCV, and a lot of the algorithms have hard constraints on the color space so they may not work with this Mat type.
A cv::Mat can have more than 4 channels even (up to 512 the last time I checked, for more info check the constant CV_CN_MAX), but beware that this may not work with all of OpenCV functions and it will more like a container to your custom algorithms.