For a short run (eg a few weeks to a few months) which might be used in a real-time system, these correlations are likely to be poorly estimated, thus it would be better to let the user supply them in the config file, perhaps as estimated for the target region based on a longer run.
Also, at present the mean correlations are calculated across all stations, but if a larger domain of stations is given in the input file than is used in the target domain, the estimate will not be optimal for the local region. It's worth calculating the correlations after the analysis to find the nearest neighbors for all the grid cells in the target domain.
Of course the bigger issue is that the full domain mean long term correlation is a huge approximation, and could be refined locally and seasonally for better results (should be another issue).