It sounds like you've got a good handle on the 990's bypass mode. The stereo bypass mode passes an unaltered signal to the mains, but if the mains are set to small a copy of the signal is sent to the subwoofer.
Gonk, your simple replies to these issues are really helpful! Still I wonder, is there any possibility the SMALL/BYPASS mode could be altered with a 990 firmware update to send unaltered signal to the mains but digitally processed bass below the crossover frequency--instead of unaltered signal--to the sub? This would be like the "950 solution" to the problem that seemed like a workable compromise.