First Sentence of that link:
Equalizers ("EQ") are not the "end-all, save-all solution." Care should be taken in proper speaker placement and room treatment before ANY equalization is performed. Remember EQ's are intended to help provide a flat response from your loudspeakers, NOT to redesign the them. Now that I have said that, I can begin.
If you don't do those first two steps, EQ don't mean diddly. That said, the multichannel EQ systems being offered in the higher-end receivers from Yamaha and Denon differ greatly from just adding an outboard, rackmount EQ.
I have seen and heard the Yamaha system set-up and tested and it's very impressive. In order to reproduce what it does, you need a tone generator, a RTA, a Spectrum Analyzer, and an accurate microphone on top of what ever outboard EQ you added. It's also way more accurate than just a SPL meter and test tones.
There's an article on the audioholics website about the auto EQ system that Denon is using in the 5805. According to that article, there's a lot more than just an Alesis EQ going on in that system. In fact, calling it just "Room EQ" doesn't begin to do it justice. Given, it is a system on a $5000 flagship receiver. I'm not surprised at all that it wasn't included on the 990.
Bottom line, treat your room before buying EQ.