Okay, so the first question is why the "fix" wasn't contained to the audio driver for the particular laptop, or at least the sound chip it used.
An even better solution would be for the driver stack to contain processing plugins that could be installed as part of the manufacturer's driver package, so that you only get the filtering when installing the drivers for a particular model.
Something else they could've done was to implement the filtering in hardware, either as a dedicated notch filter circuit or via custom firmware loaded into the the playback chip. In fact, I'll bet modern chipsets probably have a custom Eq curve manufacturers can pre-configure, so you get better sound quality from their integrated speakers.
What I can say about that is my audio playback on Windows 7, I think probably using VLC, would play bit-perfect out my Toslink port. I know this, because when I'd play HDCD bitstreams, my DAC would detect them. This doesn't happen if there's any processing, at all.