Ok. If you have a system at constant energy they are the same (all the microstates have the same probability). If you have a system a constant temperature a microstate can always correspond to different macrostates (it seems you’re not concerned about that ambiguity though).
In any case, the entropy is a property of (the ensemble of microstates that conform) the macrostate and not a property of the microstate. For a given macrostate you cannot use Gibbs entropy to talk about low-entropy and high-entropy microstates.
> 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.
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?
> And yes it changes with time; even at equilibrium.
What’s your definition of equilibrium? It’s hard for me to see what are we talking about, really.
> If balls are located on one side of the box and the thermometer is on the other side of the box. The thermometer reads nothing.
One could also say that if the balls are located anywhere within the box the thermometer reads nothing. The thermometer reading exists only when enough time has passed and the mercury-balls composite system is in equilibrium.
> When the balls increase in entropy they collide with the thermometer producing a reading.
Apparently you say that the entropy increases because the macrostate changes. But the macrostate is undefined until the balls hit the thermometer. But the entropy has to increase for the balls to move. It’s all a bit confusing, don’t you think?
Won’t the balls collide with the thermometer even if the entropy doesn’t change? It’s their movement that will take them there.
Consider your state - or any other state, for that matter - at t=0 and the state at t=1ps where the balls have advanced slightly. Is the macrostate different? How? Is the entropy different? How?