A lot of receivers can use the line and speaker level outputs at the same time, but the manuals almost always say not to. That's because of the way the circuit is designed. If the line output is connected to an amp, then the impedance of the circuit changes. That's fine if you calibrate the the line to output a strong enough signal to drive the amp to the appropriate level. But what happens then is the same signal is being used to drive the internal amp, and that can cause trouble.
I don't think he's saying that the sub has digital inputs, but left and right analog ins. I'd guess that about a third of all sub amps are set up that way. No uncommon. Some do get a 6 dB gain when both the left and right are fed the same signal. Again, not a big deal, but needs to be accounted for in calibration.
