Update after a couple days:
Still struggling to get the positioning right. The stands are too tall and don't really fit around the desk legs well, so I need the speakers 1-2 feet away from the corners of the desk. This makes the sound really distant or with some odd stereo phase issues. So I've reverted back to putting them on my little homemade bridge shelf. They are up on the Iso Acoustics stands which does really seem to help clean up the bass with the big drivers.
I briefly set them up alongside the JBL 306 monitors, and was absolutely shocked by the difference. The JBL's sounded like there are blankets over the speakers compared to the Yamahas. That's surprising because the JBL's sounded more open than the Genelecs, but the Yamahas had way more clarity and punch.
Looking at the frequency response graphs I can find now, I suppose that makes sense.
Here's the Yamaha HS7. The HS8 should have a flatter overall response with a little more bass, but wasn't tested by the same person. Notice the response is pretty flat, maybe tilting down by 1dB from 100 up to 10k:
Here's the JBL. Notice that it tilts down by about 5dB:
And here's the Genelec 8030. Again, the 8020 should be very similar with a little less bass extension. There's a tilt of about 5dB here as well:
So the other two monitors have a 5 dB tilt where the Yamahas are about a 1 dB tilt. That would likely explain the big difference I'm hearing.