There is physical meaning. But to get at it, one must first clean up the language to make it more precise. The Complete Set of Compatible Observables that is referred to is more commonly (and more helpfully) known as a Complete Set of Commuting Observables (CSCO). The collection of CSCO operators is used to define what is called the Universal Enveloping Algebra of the associated Lie algebra.
So far, this was just mathematics. The physical interpretation is that the CSCO allows one to find the Casimir invariant operators of the associated algebra. These Casimir operators are the collection of all the physical invariants of the quantum system defined through the Schrodinger Hamiltonian operator.
To help get a feel for how this works, it is best to use a concrete example. Consider the Hamiltonian for the hydrogen atom. For $x\in\mathbb{R}^3$, and ,$\nabla^2$, the Laplace operator, the Hamiltonian, \begin{equation} H = -\frac{\hbar^2}{2m}\nabla^2 - \frac{kQ^2}{|x|}, \end{equation} gives the total energy operator on the Hilbert space. This operator has an associated collection of Casimir operators, which are the complete collection of the invariants of this system. One knows without calculation from the laws of physics what these should be, for the most part. The operators that are intuitively obvious are, the total charge, $Q$, the total energy, $H$, the total momentum, $P$, and the angular momentum, $L$. But the interesting thing is that these are not all the invariants of this system. The system is not quite rotationally invariant because the Laplace operator has non-radial pieces. But angular momentum is definitely conserved.
The CSCO then brings to light that the missing connection has two pieces. The first is that the relevant operator for angular momentum is $L^2$, and not $L$. This is because the action of $L$ on an eigenfunction is complicated but the action of $L^2$ is always $L^2\psi = \ell(\ell+1)\hbar^2\psi$. While the second piece is the little known Laplace-Runge-Lenz vector named $A$. This is because while the Hamiltonian above is not quite rotationally invariant, i.e. not invariant under the Lie group $\mathcal{SO}(3)$ of 3d rotations, it is, in fact, invariant under the Lie group $\mathcal{SO}(4)$. The Laplace-Runge-Lenz vector, $A$, helps identify this fact as it is related to the constants of the motion and hence an invariant of the system. Furthermore, one has that the two vector operators contracted on each other through the 3d dot product is $A \cdot L = 0$. It was not at all obvious by looking at $H$ above that the system was invariant under 4d rotations.
In summary, the CSCO allows one to find all the Casimir invariant operators by finding the collection of all the quantum operators that commute with each other. Refining this collection allows one to find all the symmetries and hence invariants of the system by constructing the Universal Enveloping Algebra. For the example system of the Hydrogen atom, the Casimir invariants were $C_1 = A^2 + L^2$, and $C_2 = A\cdot L$. The physical interpretation of the CSCO is then the collection of all physically invariant operators of the quantum system associated to $H$.
For more detail, see Arno Bohm's book Quantum Mechanics: Foundations and Applicaitons.
Edit: I should also add that for the specific system in the original question, one should start with the operators that one knows like the total energy $H$, and the momentum $P$. But in that particular case, I cannot tell how many dimensions the system is in. To make things murkier in the Hamiltonian of the original question, the "potential", $V(x)$, is not an operator of multiplication because it is not even a function of $x$, for any number of dimensions. Normally for some real-valued, semi-bounded, and differentiable scalar $V:\mathbb{R}^d\to\mathbb{R}$ the commutation relation with the momentum operators is given by $[P,\,V(X)] = -i\hbar\,\nabla V(X)$. But when $V(x)$ is not a function, things get tricky very quickly.