Possibly Scintilla should define a new clipboard target type (eg "SCINTILLARECTANGLE") and advertise that as being available when a rectangular selection is made as well as the normal "TEXT", then when pasting, Scintilla can accept that target preferentially if its available, so Scintilla will then know its a rectangular paste. Probably would even work between two scintillas in different apps (maybe).
Just needs "somebody" to do it ;-P