$3D$ rotation matrix uniqueness
Given a $3D$ rotation matrix $R$ in a basis $B$. Can we consider $R$ as being unique in $B$? Is there any other $3D$ rotation matrix $R'$ representing the same $3D$ rotation in $B$? How could I prove that?
Note: I do not consider the rotation matrix $R'$ with inverted axis and angle as being the same as $R$.
Let's assume the matrix $R$ for a given rotation is not unique and there exists another matrix $Q\neq R$ which performs the exact same rotation. This means
$\forall \mathbf{v}\in\mathbb{R}^n:\quad Q\mathbf{v}=R\mathbf{v}$
and thus
$\forall \mathbf{v}\in\mathbb{R}^n:\quad (Q-R)\mathbf{v}=\mathbf{0}$
This means, that the null-space of $M=(Q-R)$ (the sub-space of all vectors whose image is the zero-vector) has to consist of the whole $\mathbb{R}^n$ (and therefore has a dimension of $n$, of course). The rank-nullity-theorem now states, that the rank of $M$ is the difference of its dimension and the dimension of its null-space, in this case $0$. But then again, only the zero matrix has a rank of $0$.
This means the above equation only holds for $(Q-R)=O$ (with $O$ being the $n\times n$ zero matrix), which in turn implies $Q=R$. This contradicts the assumption. So each rotation (in fact any linear transformation) in $\mathbb{R}^n$ corresponds to a unique $n\times n$ matrix (for a given base $B$, of course). Moreover each orthogonal matrix $R\in\mathbb{R}^{n\times n}$ with $\det R=1$ represents a unique rotation in $\mathbb{R}^n$ (again for a given base $B$ of $\mathbb{R}^n$).
In fact the matrix representation is even more unique than the axis-angle or quaternion representation (not to speak of the ambiguities of Euler angles), since because of the periodicity of the $\sin$ and $\cos$ used in the matrix representation you don't have the angle ambiguity, because $R(\theta)=R(\theta+2\pi k)$. And you don't even have the ambuigity of negated axis and angle (or negated quaternion) being the same rotation (which you especially outruled in your question), because their matrix represntations are in fact the same.
I think it is important to state that, althouth the rotation matrix $\mathbf{R}$ is unique for all vectors $\mathbf{v}$, for a given tuple of vectors, $\bar{\mathbf{v_A}}$ and $\mathbf{v_A}$, an infinite number of rotation matrixes $\mathbf{R}_i$ can be found that satisfies:
$ \mathbf{v_A} =\mathbf{R}_i \bar{\mathbf{v_A}} $
being $\mathbf{v_A}$ the position vector of a certain point, $A$, in the 3D space in a global frame, $\bar{\mathbf{v_A}}$ the position vector of the same point, $A$ in a local frame, and $\mathbf{R}_i$ the rotation matrix between both reference systems.
This statement is fundamental if the requirement is to obtain that rotation matrix from the tuple of arrays as it would lead to an infinity number of solutions if not considered.
For calculating $\mathbf{R}_i$ an overdetermined system of equations (with at least three tuples of arrays) must resolved using, for example, least squared methods to finally obtain that unique rotation matrix.