It's the long argument between thermodynamic entropy and information entropy.
Think of the 5-particle case for example. There is the empirical definition of entropy, carried out by measurements, and there is the statistical mechanical (or information theoretic) explanation of that definition.
In the 5-particle case, how do you measure entropy (or more precisely an entropy change)? You make the container have one wall with some mass that moves and apply a constant external force to it. That gives it a "constant" pressure. You can now measure the volume, and it will be constantly changing, every time a particle hits the wall it gets kicked upward, otherwise, it accelerates downward. The volume is fluctuating around some average value. You know P, V, N, and k, and assuming the gas is ideal, you get the temperature T=PV/Nk. Because volume is fluctuating, the temperature is fluctuating too, about some average value.
Now you add an increment of energy to the system, without changing the pressure. (isochoric work). Like with a paddle wheel that kicks one of the particles just a little bit. Thats your measured dU. Since dV=0 on average, dU=T dS gives you dS, the
change in entropy. Since T is fluctuating, dS will fluctuate too about an average. Not sure if that is exactly correct, but you get the idea.
Going to stat mech - the entropy is k ln W, where W is the number of microstates that could give rise to the specified P,V,T of the initial system and dS=k dW/W. This is information theory. For example, you could say S=k ln(2) Y where Y=log2(W) (log2 is log to base 2). Y is then the number of yes/no questions you have to ask to determine the microstate. (Actually the number of yes/no questions according to the "best" algorithm, in which each question splits the number of ways in half). This reminds me that the stat mech explanation is information theoretic.
Anyway, the two expressions will match, at least on average. If you increase your knowledge by following just one of the particles, you will have increased your knowledge of the system beyond that of just P,V,T. The statmech guy will say the number of questions has decreased, therefore the entropy has decreased. The fluctuations in T and V and dS will be able to be correlated somewhat with the fluctuations in the position and velocity of the observed particle. (assume classical for simplicity). The thermo guy will say no, this extra knowledge is "out of bounds" with respect to thermodynamics. So the statmech guy's definition and the thermo guy's definitions do not match, except when the statmech guy's definition stays "in bounds". If we stay "in bounds", then entropy is objective. But I have no problem wandering out of bounds, just to see what happens.
The whole problem of the extensivity of entropy and Boltzmann counting is solved by this. The thermodynamicist simply declares that drawing a distinction between like particles is out of bounds. The fact that quantum mechanics says this is true in principle in the quantum regime is really irrelevant. You can have the thermodynamics of a gas of elastically colliding cannonballs and declare distinguishing them out of bounds, and you're good to go.
Regarding the entropy of mixing, if you have two different particles, and the thermo guy declares that distinguishing their difference is out of bounds, and the statmech guy says that the knowledge of their difference is unavailiable, then their definitions match, entropy is objective, and the theory works. If the thermo guy doesn't yet have the ability to distinguish, the the statmech guy says that any knowledge of their difference is unavailiable, then their definitions match, entropy is objective, and the theory works. If the thermo guy can distinguish difference without going out of his pre-established bounds (i.e. by examining particles one at a time), then the knowledge guy says this knowledge is availiable, entropy is objective, and the theory works. If you have a gas of red and blue elastic cannonballs, and their color does not affect how they behave in a collision, and you accept that their color can be determined without appreciably affecting their velocity and momentum, then you can have a disagreement. The thermo guy will declare such measurements out of bounds, while the statmech guy will say that knowledge is availiable. The thermo guys theory will work, the statmech guy's theory will work, but they will make different calculations and different predictions.
The gas of cannonballs might be a gas of stars in a stellar cluster, and then its best to wear two hats.