To try to provide a slightly answer your question than my previous attempt, Michael, some of Peter's settings of Kipling were originally published by Robbins Music (the songs on the Argo albums certainly were). Robbins is now part of EMI Publishing. When the MCPS licence application is made, prior to manufacture, MCPS invoice the record label for a fee that largely goes, in this case, to EMI Publishing. Some (not sure how much) of this money will eventually trickle down to Peter's estate, I have it on good authority...

In the case of Danny Deever, according to the musical settings page of the kipling.org.uk website, the "manuscript (was) unpublished; in many cases there may be no surviving manuscript or definitive version, eg Peter Bellamy performed/recorded without music and any commitment to paper was done for him.". As the setting was not published, MCPS would not collect royalties. This would mean that anyone wanting record a version and ensure that Peter's estate benefited would have to make any royalty arrangements directly - presumably with Jenny B.