Bypass with a digital input is not an effective test of how bypass works with an analog input. There are two separate tables for Outlaw's "990 bass management matrix" - one for analog input signals and one for digital input signals .

With an analog input, bypass mode will yield a full range signal to the mains no matter how the speaker's bass management is configured (large or small). The bass management setting does determine whether or not a duplicate of that analog input is copied to the subwoofer - when the fronts are set to "small" and an analog input is set to "bypass" the 990 will send a summed copy of the full range inputs to the sub, whereas when the fronts are set to "large" and an analog input is set to "bypass" the 990 will not send anything to the sub.