To be honest, using a Data Source of type "Data Management Export Sequence", obviously wired to a DM sequence, in my opinion is so much cleaner than any alternative. The problem you mention gets easily addressed with a sprinkle of extra Transformation Rules.
This said, if you really have to use rules, there is nothing special about going cross-cube, just reference it with the "Cb" prefix, e.g. api.Data.Calculate("A#Target = Cb#SourceCube:E#SourceEntity:A#SourceAccount"). There are ways to do mappings (the "Convert*" calls), but they are complicated to set up and rarely worth the effort.
