Jab,
I would suggest using an (seperate) external EQ method for any sub, in any system. A dedicated parametric EQ analysis/implementation unit will do better than any built-in wonder on a receiver, flagship or not. The bass is usually the hardest part to get right. Some of the new Sunfire and Velodyne subs have this feature built in...SWEET!
One really has to be carefull if using a full parametric EQ device in their system when implementing "full-range" mains that will actually use the EQ-ing on the low end, possibly resulting in a detrement across other parts of the sound spectrum in the upper octaves...bass is very hungry. I believe one should always EQ the sub seperate from the rest of the system, thus I see no big problem with what Yamaha and others are doing.
An all-in-one unit like a receiver (that has the processing and power built in), will not have the control, dynamics, and headroom as a seperate amp, or even perhaps bi-amping(preferred), in a system that is parametrically EQ-ed. It just doesn't have the capabilities, so why force it? You will be playing a game of trade-offs and compromise... Just do it right and get a seperate EQ device for the sub(s).
For a good blend between the sub and the mains, one or more octaves between the two should be present for a smooth transition. If a sub is doing 20-60hz (like it should), then what would be the problem with yamaha's approach?
What kind and how many subs are you implementing? How do you have them configured and integrated into your system?
best,
