$ x = m \cos \omega t $
$ y = n \cos(\omega t - \phi) = n ( \cos \omega t \cos \phi + \sin \omega t \sin \phi )$
This is a linear system in $\cos \omega t $ and $\sin \omega t $, the system is
given by
$ \begin{bmatrix} m && 0 \\ n \cos \phi && n \sin \phi \end{bmatrix} \begin{bmatrix} \cos \omega t \\ \sin \omega t \end{bmatrix} = \begin{bmatrix} x \\ y \end{bmatrix} $
The solution (assuming $\sin \phi \ne 0 $ and $ n \ne 0 $ ) is
$ \begin{bmatrix} \cos \omega t \\ \sin \omega t \end{bmatrix} = \dfrac{1}{ m n \sin \phi } \begin{bmatrix} n \sin \phi && 0 \\ - n \cos \phi && m \end{bmatrix} \begin{bmatrix} x \\ y \end{bmatrix}$
Now, since $\cos^2 \omega t + \sin^2 \omega t = 1 $, then the equation governing $x, y$ is
$\begin{bmatrix} x && y \end{bmatrix} \begin{bmatrix} n^2 && - n m \cos \phi \\ - nm \cos \phi && m^2 \end{bmatrix} \begin{bmatrix} x \\ y \end{bmatrix} = m^2 n^2 \sin^2 \phi $
written concisely,
$ r^T Q r = c $
The principal determinants are $n^2$ and $n^2 m^2 (1 - \cos^2 \phi) = n^2 m^2 \sin^2 \phi $
So to have a positive definite matrix $Q$ , we must also have that $m \ne 0 $
If these three conditions are met, then the above equation represents an ellipse, because then the positive definite matrix $Q$ can be diagonalized into
$Q = R D R^T $
where $D$ is the diagonal matrix of $Q$'s eigenvalues, and $R$ is the rotation matrix whose columns are the corresponding (orthogonal) unit eigenvectors. Now the equation above can be re-written as
$ r^T R D R^T r = c $
Divide through by $c$,
$ r^T R E R^T r = 1 $
with $E = \dfrac{1}{c} D $
Now let $v = R^T r $ so that $ r = R v $ , then
$ v^T E v = 1 $
and this is clearly an equation of an ellipse because the diagonal entries of $E$ are both positive. Finally the vector $r$ is just a rotation about the origin of vector $v$, thus it describes a rotated ellipse whose angle of rotation is determined by the angle between the first column of $R$ and the positive $x$ axis.