You can safely use the configuration which specifies the range of dates that covers the extent of the data set. If somebody makes a plot of a missing day, they will get an empty plot or an interpolated result depending on the plot options they selected in the UI. Any calculations or time series plots done over the time range will account for the missing days.
You can force addXML to treat a long time series with a few missing days as if it were regular with no missing days with the -a:t command line switch.
Roland