For a while I was doing double batches and would treat the 2 cubes differently. Regularly I would cube hop them drastically differently, sometimes I would add Steeped specialty malts or adjuncts (belgian candy sugar) and add during the fermentation. I did a Dubbel and an american IPA in one batch by using a lot of cube hopping highish AA hops in the IPA and steeping spec malts into the Dubbel. Of course they used different yeasts. I won a comp with a black rye IPA that I brewed 2 cubes of. The first I brewed and tasted; I decided what I needed to do to make the second one just perfect and did just that using steeping of spec grains and boiling up some more late hops as well as adding some belgian candy sugar. It really worked out well.
I've often added spec grains at the end of the mash instead of the begining. I find that they come across smoother but more flavoursome at the same time. The enzymes in the mash break down different starches, complex sugars and carbohydrates, why wouldn't they be breaking down the complex sugars in the spec malts we go through so much effort in getting there in the first place?