No, it is rather vague what the original article means by "won’t mess with your underlying OS". And your "underlying OS won't mess with it" is equally vague too, IMHO. Providing some examples of "mess with" will be helpful.
So now docker messes with it?
Unless you've found a serious bug / security vulnerability, Docker doesn't mess with your OS. On OSX / Windows (and this is definitely an argument against Docker ux), it's not even running on your OS but a separate VM.
I did not mean "now docker messes with the OS", but "now docker is the one who messes with the thing in the container".