Short answer is I believe the single and twin cubes use the same wide range driver, so 2 vs 1 will be able to go louder before the driver bottoms out. You can only get so much out of a 2.5" driver after all. It is great for quiet and casual listening but when you crank it physics come in to play. There are no user adjustments on the Bose equipment, any equalization is handled internally. A major part of Bose design philosophy is to keep the interphase as simple as possible.
In addition you may be hearing the hole in the lower midrange the acoustimass systems are known for which occurs because the bass module is a bandpass design and doesn't go very high while the 2.5" wide range drivers can't reach low enough to overlap the crossover point. The wide range drivers also have a dramatic peak around 5kHz which will be emphasized when cranked and contribute to the tinny tone.