A merge stage cannot be used in this scenario because a merge stage takes no inputs. The xml documents to be merged are generated in the job itself. Also,any passive stage with both an input and output link cannot be used in an RTI enabled job.
Good point, the other stage is the link collector, which will bring them into a single stream and let you use column ordering to mix them up. You might be able to output it as a single XML document. The XML output stage may do the merge for you.