Let $\mathcal{H}$ with dimension $\dim \mathcal{H} = 2^n$ where $n \in \mathbb{N}$ be a Hilbert space describing your system of interest. This could be a Hilbert space for a system of $n$ qubits, for instance. There are two choices to be made.
- Choice of tensor product factorization$^{1}$. We can write
$$\mathcal{H} \cong \mathbb{C}^2 \otimes \mathbb{C}^2 \otimes ... \otimes \mathbb{C}^2$$
or we can write
$$\mathcal{H} \cong \mathbb{C}^{2^n}$$
or we can write a great number of other tensor product factorizations. As far as linear algebra is concerned, these are all Hilbert spaces with dimension $2^n$ and so are isomorphic, or essentially the same. All we have done is specify an additional labeling structure on the Hilbert space.
- Choice of Hilbert space basis. Given a tensor product factorized Hilbert space
$$\mathcal{H} \cong \mathbb{C}^2 \otimes \mathbb{C}^2 \otimes ... \otimes \mathbb{C}^2$$
we can further specify a labelling structure by giving each factor $\mathbb{C}^2$ a concrete basis. For example, $\mathbb{C}^2$ is two dimensional and so is spanned by two linearly independent vectors. We can label these basis vectors $\lvert +z \rangle$ and $\lvert -z \rangle$.
Entanglement is emphatically dependent on the choice of tensor product factorization. For instance, if we choose the tensor product factorization
$$\mathcal{H} \cong \mathbb{C}^{2^n}$$
entanglement cannot even be defined between subsytems because there are no subsystems! But, if we just move into another tensor product factorization
$$\mathcal{H} \cong \mathbb{C}^2 \otimes \mathbb{C}^2 \otimes ... \otimes \mathbb{C}^2$$
there are now subsystems and entanglement can exist between them.
Entanglement entropy is not dependent on the choice of basis for the tensor factors. This follows, as others remark, from the fact that matrix trace is cyclic and so invariant under conjugating the argument by unitary matrices
$$\text{Tr}(U M U^\dagger) = \text{Tr}(MU^\dagger U) = \text{Tr}(M).$$
This is actually a fundamental property of any entanglement entropy measure, so anything that you call entanglement entropy must be independent of choice of individual tensor factor basis. This is obvious after understanding that entanglement entropy is a quantity defined between subsystems, so it should only depend on the choice of labelling subsystems. And, the mathematical structure corresponding to labelling subsystems is precisely a choice of tensor product factorization.
Hence, the answer to your question is yes. This follows immediately from the more general fact that entanglement entropy is independent of the choice of individual tensor factor basis you choose to compute it in.
[1] In actuality, some tensor product factorizations are equivalent to other tensor product factorizations in the sense that the entanglement entropy in one tensor product factorization is the same as in another, equivalent tensor product factorization. Then, the correct object to consider is a tensor product structure, which is an equivalence class of tensor product factorizations. The precise definition of a tensor product structure is given on page 6 of the paper "Locality from the spectrum".