In this paper online, the author models the deformation of a medium as a diffeomorphism $ \mathbb{R}^3 \rightarrow \mathbb{R}^3$ as given by:
$$ y^i \mapsto x^i(y)=y^i + u^i(x) $$
as given by equation (1). The diffeomorphism induces a transformation of the metric
$$ g_{ij}(x) = \frac{\partial y^k}{\partial x^i} \frac{\partial y^l}{\partial x^j} \delta_{ij}$$
which is just the push forward of $\delta_{ij}$ under the diffeomorphism, as shown in equation (5).
It is stated that after the diffeomorphism, which transforms the metric from $\delta_{ij}$ to $g_{ij}$, the geodesics of the material will become curved because the metric $g_{ij}$ is non-trivial. Therefore, sound waves through the medium will now take curved paths as they are postulated to follow geodesics. However, this seems completely bizarre to me. A diffeomorphism is equivalent to a change of coordinates, so the geodesics of $g_{ij}$ will be the same as the geodesics of $\delta_{ij}$, which are straight lines, not curved. It is just now the geodesic equation will look a bit more complicated because we are working in a general curvilinear coordinate system. In fact, both metrics are flat because the curvature is invariant under diffeomorphisms, so I assume this is another reason to argue that the geodesics will be straight lines too?
My question
How can one describe a deformation of a material, something which physically affects the density of the material and the paths sound waves travel, as a diffeomorphism, something which does not change the manifold structure and can be viewed as a change of coordinates so should be unphysical?