“This plan will also cause Z, which is morally bad” is its own disadvantage/con.
″… and outweighs the benefit of X” relates to the caveat listed in footnote 3: you are no longer attacking/challenging the advantage itself (“this plan causes X”), but rather just redirecting towards a disadvantage. (Unless you are claiming something like “the benefits of X are not as strong as you suggested,” in which case you’re attacking it on significance.)
“This plan will also cause Z, which is morally bad” is its own disadvantage/con.
″… and outweighs the benefit of X” relates to the caveat listed in footnote 3: you are no longer attacking/challenging the advantage itself (“this plan causes X”), but rather just redirecting towards a disadvantage. (Unless you are claiming something like “the benefits of X are not as strong as you suggested,” in which case you’re attacking it on significance.)