Halliday & Matthiessen (2004: 570):
… and there is a slight tendency for ellipsis to be associated with change of polarity and substitution with change of modality. This tendency is more clearly marked with the clause, where ellipsis adds certainty (yes or no, or a missing identity), whereas substitution adds uncertainty (if, maybe, or someone said so); this is why, in a clause where everything is ellipsed except the modality, it is quite usual to a substitute (possibly so, perhaps so) unless the modality is one of certainty — here we say certainly (elliptical) rather than certainly so.