That reads a bit oddly to me. Bypass mode is passing the analog inputs directly to the left and right channels, with only volume control applied - by definition, there is no D/A involved. Since the sub is involved, the 990 is presumably behaving similar to the 950, which means the analog input is converted to digital and bass management applied to generate a subwoofer signal (assuming the main speakers are set to small), but the signal going to the mains never leaves the analog domain.

Upsample would presumably (based on the way the manual reads) only be applicable when using digital inputs, although it may also be applied by default to incoming analog signals that go through A/D conversion.