I completely agree. I find it funny when people say "There's no way that will make any difference" as if there's some sort of mystery or magic at work when someone says it does. Most of what people hear can and has been so easily explained, that to say that science doesn't explain it is just silly.
We make a change to our system. It looks different, smells different, seems different, whatever. Even if the output of the system is exactly the same (which in most of these cases it almost certianly is), it will sound different to us because how it sounds depends on how we process what we hear. How we process is directly affected by the change we made.
The only mystery to me is that we act like we don't know this.