I asked a similar question on the physics SE at this link but did not really get an answer so I'll ask here. My question there is a bit more detailed.
From what I have recently learned, in classical mechanics, the configuration of some mechanical systems (say, a double pendulum) can be described by a point on an n-dimensional smooth configuration manifold, $Q$. The dynamics are then often studied using Lagrangian mechanics on $TQ$, or using Hamiltonian mechanics on $T^*Q$, both of which have coordinate representations in $\mathbb{R}^{2n}$.
Long before I ever heard the word manifold, I was "doing" dynamics using some 2n "state space" variables in $\mathbb{R}^{2n}$. I know now that when using state space variables of the form $(\pmb{x},\dot{\pmb{x}})$, I'm really working with some coordinate representation of $(\text{x},\mathbf{v})\in TQ$. I could transform to some other coordinates $(\pmb{q},\dot{\pmb{q}})$ but, contrary to what I used to think, this is not actually a different state space but rather just different coordinates for the same $(\text{x},\mathbf{v})\in TQ$ (right?).
Similarly, when using state space variables of the form $(\pmb{x},\pmb{p}_{x})$ (phase space coordinates), I'm really working with some coordinate representation of $(\text{x},\mathbf{p})\in T^*Q$. I could transform to some other $(\pmb{q},\pmb{p}_{q})$ but again this is not a different phase space but just different coordinates for the same $(\text{x},\mathbf{p})\in T^*Q$ (right?).
My Question: When working directly with coordinates in $\mathbb{R}^{2n}$, we also commonly use more general "state space" coordinates which are not necessarily of the lagrangian form, $(\pmb{x},\dot{\pmb{x}})$, nor of the canonical/symplectic form $(\pmb{x},\pmb{p})$, but are rather just some 2n variables that fully define the state (for example, the classic Keplerian orbit element for the two-body problem). Are such coordinates on $\mathbb{R}^{2n}$ actually a coordinate representation for some ``state space manifold''? Or put differently, it seems $TQ$ and $T^*Q$ are two particular types of a "state space manifold" for which the coordinates and equations of motion have certain properties, but is there a more general manifold on which we can study the dynamics?
note: I'm aware that in the Hamiltonian formulation we can use some canonical transformation such that the coordinates $(\pmb{x},\pmb{p})$ are not necessarily split into "position level" coordinates and "velocity-level" coordinates. The Delaunay variables for the two-body problem are an example of this. So this would be an example of "jumbled" coordinates on $\mathbb{R}^{2n}$ which are actually just still coordinates for the same $T^*Q$.
Everything you said on your third paragraph is correct: you're just dealing with different coordinates for $TQ$ and $T^*Q$.
But what about state spaces which are not $T^*Q$ for any manifold $Q$? You're looking for symplectic manifolds: a pair $(M,\omega)$ where $\omega$ is a non-degenerate closed $2$-form. The main example is $(T^*Q, -{\rm d}\lambda)$, where $\lambda$ is the $1$-form on $T^*Q$ taking $Z\in T_{(x,p)}(T^*Q)$ to $\lambda_{(x,p)}(Z) = p({\rm d}\pi_{(x,p)}(Z))$, where $\pi\colon T^*Q\to Q$ is the bundle projection. Now, Darboux's theorem says that around any point in $M$ there are coordinates $(q^1,\ldots, q^n,p_1,\ldots, p_n)$ such that $$\omega = {\rm d}q^1\wedge {\rm d}p_1+\cdots + {\rm d}q^n\wedge {\rm d}p_n,$$so this situation is locally indistinguishable from working in $T^*Q$.
The literature on symplectic geometry and its relations with classical mechanics is extremely extensive. For a very quick introduction, my own notes might be helpful. I have included in the bibliography links for whatever I could find legally available online, so it might be a good starting point.