For the scope of your question, speaking of matrices $3 \times 2$ or vectors $6 \times 1$
is exactly the same thing.
So the question translates into:
In 6D, given a vector, may I decompose it into a linear combination of binary vectors having
$2$ ones in the first three components, and $2$ in the last three ?
There are $9$ different reference vectors, and thus the matter is to understand if they can form
a base for $\mathbb{R}^6$.
As already stated in a previous answer, the rank of the resulting $6 \times 9$ matrix $\mathbf{A}$
(whose columns are the nine different vectors)
is $5$, so you cannot represent whichever vector in $\mathbb{R}^6$,
but only the vectors pertaining to a specific $5$D subspace of it.
The null-space of $\mathbf{A}^T$ is the vector $\mathbf {n} = (-1,-1,-1,1,1,1)^T$, as it is easy to verify.
That means that all the nine vectors are orthogonal to this one,
and so that they span the subspace orthogonal to that.
The conclusion is that you can represent any vector lying in that subspace,
i.e. such that the sum of its upper half is equal to that of the lower half,
i.e. any matrix $3 \times 2$ ($\mathbf B$), such that the sum of its columns
is the same.
The example of $\mathbf B$ that you give is one those.