In bypass with analog inputs, there is no crossover applied because the signal never enters the digital domain. If the mains are set to small, the 990 will make a summed copy of the left and right channels which will then be sent to the sub.

In stereo mode with analog inputs, the 990 converts the signal to digital, applied bass management, and converts the signal back to analog.

If you use a digital input to the 990, you are by definition not using the player's DAC. Bypass mode with a digital input still uses the digital input, leaving the player's DAC out of the equation. I'm not an expert on what digital input/bypass mode really skips and what it still passes through, but I know at least that much about it.