I've tried using the Send Selection To --> interface but it doesn't paste back across the vertical selection.
Yep thats known behaviour see also #625 #841 #850 #1083 several of which were opened by or commented on by one@AdamDanischewski (mentioning no names :)
This whole thing will need to be examined if Geany ever moves to Scintilla 4 where rectangular selections have become multi-selections if I remember the Scintilla ML discussion correctly.