New version of the question: A simmetry needs to be canonical, following the first answer of this post which states:
the symmetry requirement is not necessary in the definition of canonical transformation, whereas a symmetry is by definition an (active) canonical transformation.
The geometric Simmetry generated by the Angular Momentum is $SO(3)$. By definition I need to intersect it with a Symplectic group $Sp(2n,R)$. I don't know how to do handle this.
The simmetry group generated by LRL vector $+$ rotational invariance is $SO(4)$. We can generate the $su(2)\times su(2)$ algebra without any effort and it gives us the right energy levels. This is the standard procedure when dealing with this problem, however we need to have a canonical transformation by definition. this post states that the intersection: \begin{equation} SO(4)\cap Sp(4,R) \simeq SU(2) \end{equation} Because an orthogonal and symplectic transformation in $R^{2n}$ must be unitary. However this leaves us with a trouble: we don't have the right algebra to build 2 different Casimir Operators and generate the right degeneracy of the system. As we know from Noether Theorem, there is a connection between degeneracy and symmetries and we looked for a different conserved quantity from L, exactly for this discrepancy.
This leads us to my issue. If the symmetry - the right one - of the system, generates the right degeneracy: why the intersection of momentum $+$ LRL vector with the symplectic group leads us to the wrong degeneracy?
Text before the edit: As far as I know the Hamiltonian is preserved under canonical transformations. These can be viewed as elements of the symplectic group $\operatorname{Sp}(2n,R)$.
Picking the hydrogenic Hamiltonian we spot a geometric symmetry $\operatorname{SO}(3)\simeq\operatorname{SU}(2)$ and a dynamic symmetry $\operatorname{SO}(4)\simeq\operatorname{SU}(2)\times\operatorname{SU}(2)$.
The latter gives us 2 different Casimir operators whose relations offer the right energy levels.
However I just read not all $\operatorname{SO}(4)$ transformation are canonical (I wonder why), so we must intersect as follows: \begin{equation} \operatorname{SO}(4)\cap\operatorname{Sp}(4,R) \simeq\operatorname{SU}(2) \end{equation} The reason lies in the fact every orthogonal and symplectic group is unitary.
However this falls in the geometric symmetry. Is it wrong? Were is the issue?