I agree with all of what you say about macro versus micro. It's the whole "river" analogy -- you can splash about all you want and create some local ripples, but the steady flow of the river very quickly erases any record of your presence.
Sort of.
The reality is that the ripples we create are part of a dynamic system, but that dynamic system follows strict rules. In theory, if you had a powerful enough computer and the ability to track precisely each and every molecule, including precise information on speed and location of each and every molecule, you could reverse engineer every single ripple that ever happened in that river in the past as well as the future, because the system is roughly the equivalent of a hologram in its ability to store a record of every interaction that ever happened with it.
Sort of.
Because, you notice, I said "precise information on speed and location", and that's where the whole quantum indeterminate issue starts to affect the whole system. Imagine one molecule being in a slightly different place -- won't have macro effects today, but that will start a ripple, a chain of events that will get steadily larger, and if you looked at the outcome 5 years from now, the river might actually be running differently than it would have had that molecule not been in a slightly different place. It's the whole butterfly effect thing. You can't actually predict its exact state 5 years from now because those small indeterminacies start to have larger and larger effects the longer the system runs. It's like a rifle whose position you change by a fraction of a millimeter -- the location of the bullet 1 inch from the gun will not be detectably different, but you go out 2 miles and suddenly that bullet is 2 feet off from where it otherwise would have been.
I sense that you and the other article you reference are equating free will with the ability to do whatever we want without those choices being affected in any way by the system, but that is only one definition of free will. Another definition would be that there is nothing outside of the system that forces the system to stay in any particular configuration -- and that, I believe, we do have.
Have you ever read anything about the effect of intention on random number generators, or the effect of "healers" of many different belief systems on medical outcomes?