Well the theory of the balance tube has to do with sound wave propagation and frequency. Obviously Yamaha thought it was important at one time through there R&D. I don't think this theory was tested on our machines with all these aftermarket goodies, ported and polished cylinders, big bores, long rod cranks, larger carbs, aftermarket filters, etc. I'm sure these modifications would change the sound wave frequency in the intake tract. So can we really assume that a balance tube or even a boost bottle should make an improvement on anything other than a stock machine that it was R&D'd for? Who knows, if it works for you, use it, if it doesn't then see The Rail's thread on "best use for a boost bottle" .
P.S. Looks like the spacers crispened the throttle response up a bit, at a cost though.