In general, alternative answers are for when you want to try marking the same answer with different part settings. The gap-fill part only really has one setting, "sort student's answers before marking", but you might also use it to try a different custom marking algorithm.
I think what you want to happen is best done with a custom marking algorithm: you could change the `gap_order` note in an alternative to mark the gaps in the order (x2,y2), (x1,y1). If the gaps are defined in the order x1,y1,x2,y2, you'd put this in a custom marking algorithm:
gap_order: [2,3,0,1]
I hope that helps!