Yes, I realize that this game breaks down when it comes to throwing Fistfuls of Dice, but green dice don’t cancel purple dice, and yellow dice don’t cancel red dice.
There's already a cap on all those, you can't get more than 6 on either side. The dilemma comes from being able to purchase items and abilities which give you a ton more Boost / Setback dice to work with in addition.
In that case, I would suggest putting a cap on the total number of Boost or Setback dice that are allowed, instead of having them cancel each other out.
Of course, with enough upgrades, I can still fairly easily get up to eight or nine yellow dice in a roll, even if the cap for Attributes is 7 (including cybernetics) and the cap for Skills is 5.