Hello Helsky,
Already two years have past since that topic. PhotoScan is already using full color range of the images.
But I think that you have mixed several questions into the single topic, so I'll try to underline some important points related to your questions.
A) Texture generation and orthophoto export are independent processes. Orthophoto generation doesn't take into account previously create texture, even the model can remain untextured up to orthophoto export step.
So mapping modes used in Build Texture dialog shouldn't bother you, unless you are interested in producing textured mesh model as output.
B) Texture size and count parameters defines the pixel dimensions of the texture atlas and number of texture atlas pages (the latter is only applicable for Generic mapping mode).
C) Multichannel TIFF images with four and more channels in the version 1.0.4 are treated differently from the common three-band images. At first user defines Master Channel in the chunks' context menu in the Workspace pane, that will be used for the alignment stage and dense cloud generation stage (also note that texture generation cannot produce multichannel texture atlas and only Master Channel will be used).
But at the Export Orthophoto stage, if TIFF format is selected, the resulting ortomosaic will contain all the original channels.