Currently there is no batch access for FLAASH. You can use Quac as an alternative which does have batch access. As for your second question, I found this discussed in a paper by SSI: As discussed elsewhere, up to an order of magnitude improvement in speed can be obtained by using an approximation in which the convolved reflectance and water vapor are averaged within pixel groups (“superpixels”) and Eq. (1) is reduced to a simple linear form [Matthew et al., 2000]. This method, implemented with 4x4 superpixels, is the default in FLAASH, and is suitable for sensors that have a spatial resolution finer than the typical ~100 m distance of the adjacency point spread function. I believe this to mean a 4x4 window over the pixel of interest, or 16 pixels total for the calculation.