Here $d\leq M$ and we work over $\mathbb{R}$. Your definition of $Gr$ is false; the $X$ must have full rank. On the other hand, it's not a good parametrization; you must add the quotient by the equivalence relation: $X\sim X'$ if and only if $X'=Xh$ where $h\in GL_d$.
Consider the canonical functions
$$f:O(M)\rightarrow St(d,M),g:O(M)\rightarrow Gr(d,M),h:St(d,M)\rightarrow Gr(d,m).$$
Since $f$, $g$, and $h$ are submersions, we deduce that
\begin{align}
St(d,M)
&\sim O(M)/O(M-d),Gr(d,M) \\
&\sim St(d,M)/O(d) \\
&\sim O(M)/(O(d)\times O(M-d)).\end{align}
Note also that $Gr(d,M)\sim Gr(M-d,M)$ and have dimension $d(M-d)$.
EDIT. Answer to OP. The problems
$$\min_{U\in St(d,N)}\langle UU^T,L\rangle+\beta \|UU^T\|_1$$
and
$$\min_{U\in Gr(d,N)}\langle UU^T,L\rangle+\beta \|UU^T\|_1$$
are equivalent under the condition that a representative of $U\in Gr$ is one of its orthonormal bases.