As discussed in the source, video and audio are in practice seldom divorced. It was intended as a real-world test, and real-world it was. As mentioned, the sound quality in the Ogg version was better than in the YouTube version. You're good with lower sound quality in exchange no/little change in video performance? (Usually, audio is the thing people are more sensitive to!)
"YouTube encoded just H.264 baseline profile while the Theora encoding was tweaked to be optimal."
Yes, it was in answer to "YouTube can't use Theora." It naturally used YouTube to compare against.
"Still the resulting quality is better and the file smaller..."
Actually, the Ogg bitrates were slightly lower (486 vs 490kbps, 325 vs 327kbps).