This is a partial answer.
This answer proves that if $N$ is prime, then $S_{n-2}\equiv 0\pmod N$.
Proof :
First of all, let us prove by induction on $i$ that
$$S_i=s^{3^{i+2}}+t^{3^{i+2}}\tag1$$
where $s=2-\sqrt 3,t=2+\sqrt 3$ with $st=1$.
We see that $(1)$ holds for $i=0$ since
$$S_0=P_9(4)=2^{-9}((4-2\sqrt 3)^9+(4+2\sqrt 3)^9)=s^{3^2}+t^{3^2}$$
Supposing that $(1)$ holds for $i$ gives
$$\begin{align}S_{i+1}&=S_{i}^3-3S_i
\\\\&=(s^{3^{i+2}}+t^{3^{i+2}})^3-3(s^{3^{i+2}}+t^{3^{i+2}})
\\\\&=s^{3^{i+3}}+t^{3^{i+3}}\qquad\square\end{align}$$
Using $(1)$ and $N=4\cdot 3^n+1$, we have
$$S_{n-2}=s^{3^{n}}+t^{3^{n}}=s^{(N-1)/4}+t^{(N-1)/4}$$
Noting that
$$\sqrt{2\pm\sqrt 3}=\frac{\sqrt 6\pm\sqrt 2}{2}$$
we have
$$S_{n-2}^2-2=s^{(N-1)/2}+t^{(N-1)/2}=\left(\frac{\sqrt 6-\sqrt 2}{2}\right)^{N-1}+\left(\frac{\sqrt 6+\sqrt 2}{2}\right)^{N-1}$$
Multiplying this by $2^{N+1}=2^{N-1}(\sqrt 6-\sqrt 2)(\sqrt 6+\sqrt 2)$, we get, by the binomial theorem,
$$\begin{align}&2^{N+1}(S_{n-2}^2-2)
\\\\&=(\sqrt 6+\sqrt 2)(\sqrt 6-\sqrt 2)^N+(\sqrt 6-\sqrt 2)(\sqrt 6+\sqrt 2)^N
\\\\&=\sqrt 6\ ((\sqrt 6-\sqrt 2)^N+(\sqrt 6+\sqrt 2)^N)
\\&\qquad\qquad -\sqrt 2\ ((\sqrt 6+\sqrt 2)^N-(\sqrt 6-\sqrt 2)^N)
\\\\&=\sqrt 6\sum_{i=0}^{N}\binom Ni(\sqrt 6)^{N-i}((-\sqrt 2)^i+(\sqrt 2)^i)
\\&\qquad\qquad -\sqrt 2\sum_{i=0}^{N}\binom Ni(\sqrt 6)^{N-i}((\sqrt 2)^{i}-(-\sqrt 2)^{i})
\\\\&=\sum_{j=0}^{(N-1)/2}\binom{N}{2j}\cdot 6^{(N-2j+1)/2}\cdot 2^{j+1}
\\&\qquad\qquad -\sum_{j=1}^{(N+1)/2}\binom{N}{2j-1}\cdot 6^{(N-2j+1)/2}\cdot 2^{j+1}\end{align}$$
Here, using that $\binom Nm\equiv 0\pmod N$ for $1\le m\le N-1$, we get
$$2^{N+1}(S_{n-2}^2-2)\equiv 2\cdot 2^{(N+1)/2}\cdot 3^{(N+1)/2}-2^{(N+3)/2}\tag2$$
Since
$$4\cdot 3^{2k}+1\equiv 4\cdot 1+1\equiv 5\pmod 8$$
and
$$4\cdot 3^{2k+1}+1\equiv 12\cdot 1+1\equiv 5\pmod 8$$
we see that
$$N\equiv 5\pmod 8$$
from which we have
$$2^{(N-1)/2}\equiv \left(\frac{2}{N}\right)=(-1)^{(N^2-1)/8}=-1\pmod N\tag3$$where $\left(\frac{q}{p}\right)$ denotes the Legendre symbol.
Using $2^{N-1}\equiv 1\pmod N$ and $$3^{(N-1)/2}\equiv\left(\frac{3}{N}\right)=\frac{(-1)^{(N-1)/2}}{\left(\frac N3\right)}=\frac{1}{1}=1\pmod N$$ we get, from $(2)(3)$,
$$4(S_{n-2}^2-2)\equiv 2\cdot (-2)\cdot 3-(-4)\pmod N$$
from which
$$S_{n-2}\equiv 0\pmod N$$
follows.$\quad\blacksquare$