I've been following Gil Strang's lectures and he shows that $Null(A)$ is orthogonal to $Row(A)$ of an $m\times n$ matrix $A$ from the fact that matrix multiplication $Av$ is like taking the dot product of $v$ with the rows of $A$, or $Av=\begin{bmatrix}r_1v\\\vdots\\r_mv\end{bmatrix}$. If $v$ is in the null space, every $r_iv=0$, so $v$ must be orthogonal to the span of the rows of $A$. He uses a similar logic to show orthogonality of $Col(A)$ and $Null(A^T)$.
To me this only makes sense if $v$ and $r_i$ are seen as vectors in the standard basis. If $v$ has coordinates based on some arbitrary basis of $R^n$ (I don't even know what coordinates $r_i$ would be in terms of in this case), the dot product of the coordinates of two orthogonal vectors may not equal 0. However, $Av = 0$ ($Null(A)$) is still $v$ such that every $r_iv=0$. Is there a more general way to see orthogonality of the fundamental subspaces that is basis independent?