Does "every other application" include WPF apps? If not then you can play with the Avalon.Graphics user settings as you please, these setting don't affect Win32/GDI rendering.
That's what I did actually, to me it seems that either the ClearType tunner writes the wrong WPF settings or that WPF interprets them wrongly. I tried your ClearType settings (from the tunner screenshot) and I ended with EnhancedContrastLevel being set to
The WPF apps I use include a Twitter client and the PowerShell IDE. Those have the pixel-snapping issue but not this boldness/fuzziness issue. Changing CT settings make those totally unbearable.
But I can install Windows without a key and get a month to play with the settings. I will try that.