MergeOmatic is using RE functionality to merge records. The RE function does not currently offer the ability to deselect addresses from the merge fields.
Note: At this time, Blackbaud's Development team has determined that future implementation of a product change for this issue is not likely. Should their determination on this issue change in the future, clients will be alerted via release notes for the specified product. In this case the specified product is The Raiser's Edge.