I looked at the letter and I don't think the situation is that bad. The LW says they've met the twin sister "several times" but don't know her well; and also that their plan is to give the brother "a check for graduation." Amy counters that they should give the twins each a "modest" gift for graduation, then separately give the boy a "bonus" for his work for them; and she also suggests that they wait and give him this bonus gift not at graduation time, but rather just before he leaves for college (so, maybe at the end of the summer).
I think that sounds like a good idea. If they were totally unacquainted with the sister, it wouldn't be odd to give her nothing and her brother a check for $100; but since they do know her, and seem to be planning on giving her something as a graduation gift ("Should our gift to her be the same amount?"), it would be weird to give the brother a check for $100 and the sister a check for only $15 (or whatever).
I think it avoids awkwardness to give them both identical "words of wisdom for recent graduates" books (my dad's favorite graduation gift), and then later on, at a separate occasion, to give the brother a check with a nice note about how much they appreciate what he's done for them and how well they think of him.