$M$ is always a submanifold.
As you suggested, we can look at the space $\tilde{\mathfrak{g}}$. However, $\tilde{\mathfrak{g}}$ is not diffeomorphic to $\mathcal{F}$. Rather, it is a quotient of $\mathcal{F}$.
More specifically, we have:
Proposition: Let $N = N_G(T)$ be the normalizer of $T$ in $G$. Then $\tilde{\mathfrak{g}}$ is diffeomorphic to $G/N$.
Proof: As you noted, $G$ acts transitively on $\tilde{\mathfrak{g}}$, so we only need to determine the stabilizer at a point. Consider a point $\mathfrak{g}_x$ with $x\in T$, $g\in G$ stabilizes this set iff $Ad_g(\mathfrak{t}) = \mathfrak{t}$ (where $\mathfrak{t}$ denotes the Lie sub-algebra of $T$). Exponentiating out, we find that conjugation by $g$ stablizes $T$, so $g\in N$. Conversely, if $g\in N$, then $g$ stabilizes $T$, so $Ad_g$ stabilizes $\mathfrak{t}$. $\square$.
Simply because $G/N$ is easier to type, I'll stop writing $\tilde{\mathfrak{g}}$ and instead right $G/N$ for the duration of this post.
Note that since $T\subseteq N$, we have a natural projection $\pi:G/T\rightarrow G/N$. This projection is actually a covering with $|N/T|$ sheets. (More generally, the projection is a fiber bundle with fiber $N/T$, but in the case of compact Lie groups, it is well-known that the Weyl group $N/T$ is finite.)
Proposition: The $\theta$ action on $G$ induces a $\theta$ action on $G/N$. Under the diffeomorphism $G/N\rightarrow \tilde{\mathfrak{g}}$ this $\theta$ action is equivariantly diffeomorphic to the $\theta$ action on $\tilde{\mathfrak{g}}$ given by $\mathfrak{g}_x\mapsto \theta(\mathfrak{g}_x)$.
Proof: Define $\theta(gN) = \theta(g)N$. To see this is well-defined, let $n\in N$. Then $\theta(n) \in N_G(\theta(T)) = N_G(T) = N$, so $$\theta(gnN) = \theta(gn)N = \theta(g)\theta(n)N = \theta(g)N.$$
For the second statement, consider the diffeomorphism $\psi:G/N\rightarrow \tilde{\mathfrak{g}}$ given by $\psi(gN) = Ad_g \mathfrak{t}$. Then $$\psi(\theta(gN)) = \psi(\theta(g)N) = Ad_{\theta(g)} \mathfrak{t} = Ad_{\theta(g)} \theta(\mathfrak{t}) = \theta(Ad_g \mathfrak{t}) = \theta(\psi(gN)).$$
$\square$
The induced $\theta$ action on $G/N$ is obviously an involution, so, as you already know, this implies $\mathrm{Fix}(\theta)\subseteq G/N$ is an embedded submanifold of $G/N$.
But we also obviously have that $M = \pi^{-1}(\mathrm{Fix}(\theta))$. Thus, to finish off the proof, we need only note that the inverse image of a submanifold under a covering is itself a submanifold. Indeed, slice charts on $\mathrm{Fix}(\theta)$ pull back to to slice charts on $M$.