I haven't ever used spotify, so forgive my ignorance. How are they measuring the system volume from inside a webapp? Shouldn't that information not be visible to them?
It pauses it if you put the in-app volume too low. I think the desktop client also reacts to the system volume setting, but it's been a while since I had the free plan.
I have this issue with the NPR One web player on Windows7. When the laptop is muted and I press the physical button to unmute it, the mute light goes off, but the web player soft-mutes. Argh.
Why can’t the mute button just be a physical switch!?!?!?
You could try getting a 3.5mm stereo cable, cutting the end off and using that as your physical mute button. Not sure if that routes audio to the "headphones" at the software or firmware level, but anything reading volume levels would still see it set to whatever level the OS is at.