Let's say you have standard basis $\beta = \{ (1,0), (1,0) \}$ for $\mathbb{R}^2$ and linear transformation $T: \mathbb{R}^2 \to \mathbb{R}^2$ that is diagonalizable with two distinct eigenvalues, so you have a basis of eigenvectors $\gamma = \{ w_1, w_2 \}$.
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 $\gamma$ and they will be orthonormal.
To be concrete, I mean that $[w_1]_\gamma = (1, 0)_\gamma$ and likewise for $w_2$.
So does orthogonality fully relate to the notion of what basis you are using, and any basis you choose can be made orthogonal simply by choosing that basis as reference?
This doesn't make complete sense to me, since we have the G-S process, and this seems to make the notion of orthogonality almost useless if this is the case.
So when we say that for a finite dimensional inner product space $(V, \langle \cdot , \cdot \rangle)$ over some $\mathbb{F}$, do we define this notion of orthogonality (when $\langle x , y \rangle = 0$ for $x, y \in V$) as independent of basis?
Arbitrary linear transformation do not preserve orthogonality. "Expressing a vector in the basis $\gamma$" is a linear transformation $\phi_\gamma : \mathbb R^2 \to \mathbb R^2$ with $\phi_\gamma(v) = [v]_\gamma$. Linear transformations which preserve the inner product (and hence orthogonality) are called orthogonal transformations, and are represented by orthogonal matrices relative to an orthogonal basis. $\phi_\gamma$ is not orthogonal because it takes a nonorthogonal basis ($\gamma$) to an orthogonal one (the standard basis).
As you say, orthogonality is defined via $\langle x,y\rangle = 0$. This has nothing to do with a basis. "Preserving the inner product" for linear $T : \mathbb R^2 \to \mathbb R^2$ means $$ \langle Tx, Ty\rangle = \langle x,y\rangle $$ for all $x,y\in\mathbb R^2$, so this is the formal definition for "$T$ is orthogonal". This also has nothing to do with a basis. You will find that $\phi_\gamma$ does not satisfy this condition for the standard inner product.
Just because nonorthogonal transformations exist does not mean that orthogonality is useless.