The receiver's stereo analog inputs (not a stereo signal to the multichannel input) are converted to digital and then become functionally identical to a PCM stereo signal coming via a coaxial or optical digital cable.

I would either disable the sub's crossover or set it to its highest setting because you already have a bass management system in place that is redirecting bass from other channels into the sub and merging them with the LFE channel. You don't need to sub's crossover, and if it is set anywhere near the crossovers in the HTPC or receiver then you will start to stack crossovers (thus losing some low frequency data in the vicinity of the crossovers, since none of the crossovers are "brick walls" and all have a slope associated with them that creates some influence both above and below the set crossover point).