The custom column configuration system built for batch item modification and batch item deletion predates the addition of DataTable column configuration. I don't think there's any reason to keep it, and making things standard is good.
That would be nice ! When we hide columns in batch item modification/batch item deletion, the hiddens columns will stay hidden in the next batch modification or deletion (tho currently there's a bug for that in bz32477). But when our browser cache is renewed, those choices are reinitialised and all the colums are showned. Having the choice to permanently hide some columns by adding those tool to the column configuration would save time when we always hide one or more columns.