The eigenvectors are not guaranteed to be orthogonal, and if you use G-S, they may no longer be eigenvectors. However, you can always write the eigenvectors in terms of the basis γ
and they will be orthonormal.
You are confusing a vector in $V = \mathbb R^2$ with it's coordinates (also in $W = \mathbb R^2$)! Consider a general vector space $V$ with an inner product which is a map $ V \times V \to V$. This map is defined for $V$ and not for the space $ W = \mathbb R^{\dim V}$ obtained by fixing a basis. You can only take the dot product between vectors in the vector space $V$. That is, the dot product is base independent !
What you are doing is taking two basis vectors $w_1,w_2$ looking at their coordinates in the basis $\gamma$ and taking the dot product of their coordinates as if they were points of the vector space $V$. But the coordinates are in the space $W$ which is not equipped with a dot product.
If you want to equip $\mathbb R^{\dim V}$ with a dot product then the only natural way to do so is to define a map $\phi_\gamma : V \to \mathbb R^{\dim V}$ which maps $v$ to it's coordinates in the basis $\gamma$ and define the inner product on $\mathbb R^{\dim V}$ by
$$ \langle \phi_\gamma(v), \phi_\gamma(v')\rangle_{\mathbb R^{\dim V}} := \langle v,v' \rangle_{V}$$
Doing so in your example you will see that the dot product of $[w_1]_\gamma = (1,0)$ and $[w_2]_\gamma = (0,1)$ is not
$1 \times 0 + 0 \times 1 = 0$ but is by definition the dot product of the vectors $w_1,w_2$. This is because the dot product is by definition
$$ \langle [w_1]_\gamma, [w_2]_\gamma \rangle := \langle w_1, w_2 \rangle $$
In order to avoid confusion it is probably best to use a different notation for coordinates. You might want to write the coordinates of a vector as a column vector.
For a specific example suppose that $w_1 = (0,1)$ and $w_2 = (1,1)$ and $V = \mathbb R^2$ defined with the usual dot product. In the basis $\{w_1,w_2\}$ the basis vectors have the coordinates $(1,0)^T$ and $(0,1)^T$. And a point of coordinate $(x,y)^T$ cooresponds to the point in $V$ defined
as $ xw_1 + yw_2 = (y,y+x)$. It follows that the dot product on the coordinate space is defined by
\begin{align*}
\langle (x,y)^T,(x',y')^T \rangle &= \langle (y,y+x), (y',y'+x') \rangle \\
&= yy' + (y+x)(y'+x').
\end{align*}
This means that $\langle (1,0)^T,(0,1)^T \rangle \neq 1 \times 0 + 0 \times 1$. Rather $$ \langle (1,0)^T,(0,1)^T \rangle = 0 \times 1 + (0+1)(1+0) = 1. $$
self-adjoint
andnormal
for an orthonormal eigenbasis to exist, and I wanted to first get a better understanding of how orthogonality relates to basis. $\endgroup$