Ok. I'm glad to read that we finally agree that in your example -using the macrostate you defined- the entropy of the "particles near a corner" state is not different from the entropy of any other "particles not near the thermometer" state.
Right after you said "Temperature as measured by a thermometer is the macrostate. Every possible configuration of particles (microstates) that causes mercury to rise to a certain degree represents a different macrostate." - I asked "How does your configuration where the balls where near one corner in the cube causes mercury to rise to a different level than the configuration where they occupy a larger volume near the center?"
You could have answered "it doesn't - that's the same macrostate with the same temperature and the same entropy" back then.
Later I pointed out that "Reducing the space occupied by the initial configuration [doesn't change] the temperature - which you say is 0 in all those cases - or the macrostate - which you call absolute zero macrostate in all those cases. The entropy would be the same whenever the particules are more concentrated than in your example - even though they would have lower probability of ocurrence. Don't you agree?"
Instead of answering "I don't agree. Entropy is lower when the current macrostate has a low probability of occuring." you could have said "I agree. I describe the temperature as zero in all those cases, it's the same macrostate and the entropy will be the same."
Better late than never, anyway.
> the word temperature is poorly defined when applied to a box.
I agree! You're the one who picked the reading of that thermometer as the thing that would determine the macrostate and the entropy - and maintained that higher concentrations would mean different thermometer readings and lower entropy.
> If you are in agreement with me that entropy is independent of knowledge then we're good; because as far as I was concerned this was the point you were trying to make.
If we agree that the entropy is not a physical property of (the microstate of) the system but a property of a particular (thermodynamical) description of the system - and that different descriptions of the same physical system are possible resulting in different entropies - we're good. That's the clarification I wanted to make.