First off, while $\alpha$ and $\beta$ can indeed be represented by matrices (of $2 \times 1$ size, not of $N \times O$), it can not be done for spatial orbitals $\psi$, and consequently, for spin orbitals $\chi$ as well. Thus, the last paragraph of your question does not make sense.
Secondly, everything is pretty simple here, so you do not need any matrix representation. The thing you have to understand is that when you use Dirac bra-ket notation with spin orbitals you integrate over both spin and spatial coordinates of electrons, i.e.
$$
\langle \chi_{2i-1} | \chi_{2i} \rangle
=
\iint \chi_{2i-1}^{*}(\vec{x}) \chi_{2i}(\vec{x}) \mathrm{d}\vec{r} \mathrm{d}\omega \, ,
$$
where integration over $\mathbf{R}^3$ is assumed for spatial coordinate $\vec{r}$. Now if you express spin orbitals as mentioned in the question you get
$$
\langle \chi_{2i-1} | \chi_{2i} \rangle
=
\iint \phi_{i}^{\alpha *}(\vec{r}) \alpha^{*}(w) \phi_{i}^{\beta}(\vec{r}) \beta(\omega) \mathrm{d}\vec{r} \mathrm{d}\omega \, ,
$$
and the double integral clearly breaks into the following product of two singe integrals
$$
\langle \chi_{2i-1} | \chi_{2i} \rangle
=
\int_{\mathbf{R}^3} \phi_{i}^{\alpha *}(\vec{r}) \phi_{i}^{\beta}(\vec{r}) \mathrm{d}\vec{r} \int_{-1/2}^{+1/2} \alpha^{*}(w) \beta(\omega) \mathrm{d}\omega \, .
$$
The second integral in the product is zero by definition of spin functions $\alpha(w)$ and $\beta(\omega)$.
This way you prove that if two spin orbitals "come from different worlds" (one from "$\alpha$-world" and another from "$\beta$-world") they are orthonormal, since the second part of the product above is zero. If two spin orbitals "come from the same world", then the first part of the product above will be zero, since spatial parts of spin orbitals from "the same world" are orthonormal as stated ath the very beginning of the question. And again spin orbitals are orthonormal.