I think that when the original story was writen the developers could have come up with "Well we are agoing to kill this character off." They didn't know exactaly when or how they were going to do it, just that they were. This would explain why they needed extra dialog. When they started actually creating he game thay had a better idea about when they would kill off Aeris so that's why the rest of the game is not FILLED with lines for her but just has a smattering.

They could have also changed the layout of the storyline so that those extra parts (I thought I read somewhere that one extra set of lines was after the snowboard segment) were really in the game before she died. When they moved the story around it was just easier to (basically) copy/paste the code to a new place. Who cares if the extra Aries lines are there noone would Normally see them anyway.

Also I suppose some Square coder could have just put them in for fun. No one would be looking for Aries text becuse she was dead by then. Whick of course would have made them stand out once/if found.