Let's lay all the groundwork here:
First - Regardless of THD rating you won't be able to discern a difference between these two amplifiers without going beyond one or the other's capabilities (IE Clipping). Distortion isn't audible to humans unless it exceeds 1%, both of those components are far under that distortion rating so they are both going to put out exactly what goes in giving you clean, undistorted, and color free amplification.
Second - Just because the DSP-3090 is rated 85 watts per channel doesn't mean each channel has a cap limit of 85 watts. Normally such ratings are closer to an ACD rating (all channels driven) and doesn't reflect what one or two channels may be capable of outputting at any given moment. A integrated home theater amplifier like the DSP-3090 may be capable of outputting more than 200 watts from one channel at any given moment because each bi-polar transistor set is usually rated much higher than the specified wattage per channel rating. On the DSP-3090 I would assume that the specified output of a single output transistor to be higher than 200 watts, they do this to allow one channel to deliver more power when it's needed as well as protect the circuit from frying from too much power. The power supply, transformer and capacitors primarily, are big enough on the DSP-3090 to make it a formidable 2 channel system (which is what I like about multichannel amplifiers and receivers).
You see, because the system is meant to handle 5 or more channels of power the transformer and capacitors are often bigger than a similarly rated stereo receiver, and more often than not have far great headroom than a stereo receiver of similar rating. My guess is that if you where to benchtest the DSP-3090 which has a similar amplifier to the DSP-1000 (a very stout unit) that with 4 ohm loads with 2 channels driven at or under the specified THD that it would output around 200 watts per channel ore more, it may even do this at 8 ohms. I've looked closely at the output stage on the DSP-1000 and the transistors are quite large and indeed capable of handling some heavy duty stuff. The transformer is one of the largest iron core transformers I've seen in such a component and the 2 capacitors are nearly as large as cans of Redbull which if I recal correctly where 15,000uF a piece.
Needless to say it's got enough power to drive most speakers to ear bleading levels without stress unless you are talking about driving speakers with super low sensitivity and extremely reactive loads.
Third - The MX-1000 is a fine amplifier. Be sure that you understand that just because it has outputs for 3 separate banks of stereo speakers that each output has it's own dedicated output. Bi-amping from there would be more like Bi-wiring, which is a complete waste of time and wire.
Fourth - You could effectively bi-amp by using both the DSP-3090 and MX-1000 since you have already confirmed the input sensitivity for both the on board amplifier and MX-1000 are the same, however you might find that if you pushed too hard you may accidentally start losing drivers due to overpowering them. The specifications indicate that you should power the RTi 12 with anything from 50 watts - 500 watts per channel. To power these speakers with a 500 watt per channel amplifier is absolutely unnecessary for almost every application. Even in an active x-over array the low end drivers would be the first to go unless you put a subsonic filter on them and replaced the low end support with a couple of heavy duty subwoofers that would be able to keep up with such a tremendous level of output.
Fifth - I would suggest keeping the MX-1000 is it's output capability is obviously beyond the DSP-3090 and will certainly have twice the headroom with twice the capacitance. Use the MX-1000 in conjunction with whatever new receiver or preamp/processor you happen to get.
Sixth - Let me know what you plan to do with your DSP-3090, I may have a specific use for it should you decide to let it go. I just picked up a pair of Vandersteen 2Ce towers and would like to have good clean power in a single component as well as have the function of an RF AC-3 input so I can utilize my laserdisc player's full potential.
Good luck!
