The RYA booklet C4 on Flag Etiquette and Visual Signals is an interesting useful and inexpensive guide to flag etiquette and a handy source of reference to flag signals. See here
There is no suggestion in that booklet that the mizzen mast of a ketch or yawl should or could be used as the alternative position for the burgee although it is one of the alternatives for the Ensign. As Searush says the accepted alternative for the burgee is the starboard cross-tree but that brings it into conflict with a courtesy ensign. Reading the booklet it seems to infer that a courtesy ensign would be hoisted below it but I know others will not agree.
Logically though it would seem that the mizzen mast would be an alternative to the main mast head, being inferior to the flag staff in the stern but superior to the starboard cross tree. thus preserving the order of superiority of the flags. Namely Ensign, burgee then courtesy Ensign.
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