I will use the set up of my answer to a previous question about "Fibonacci polynomials".
The key observation is that the coefficient of $x^m$ in $P(x)$ equals the number of "unrollings" of the Zeckendorf representation $Z_m$ (viewed as a $01$-string) of $m$, where any substring $001$ can be unrolled into $110$. Let $U(Z_m)$ denote the number of such unrollings. It is easy to see that $$U(0^p1v) = U(v) + \left\lfloor\frac{p}2\right\rfloor U(0v).$$
Then one can notice that $$\nu_k(n) = \nu'_k(n) + \nu'_k(n-1) - [k=1],$$ where $\nu'_k(n)$ is the number of coefficients of $x^m$ in $P(x)$ equal $k$ with $m<F_{n+2}$ (ie. $|Z_m|\leq n$). Here the Iverson bracket $[k=1]$ eliminates double counting of $v=0^n$ and $v=0^{n-1}$, which both correspond to $m=0$ .
The aforementioned recurrence for $U$ allows us to obtain one for $\nu'_k(n)$ as follows.
Let $a_1(n,k)$ be the number of strings $v$ of length $n$ starting with 0 such that $U(v)=k$, and let $a_2(n,k_1,k_2)$ be the number of strings $v$ of length $n$ starting with 0 such that $U(v)=k_1$ and $U(0v)=k_2$. Clearly, $a_2(n,k_1,k_2)=0$ whenever $k_1>k_2$ and we find it convenient to assume that both $a_1$ and $a_2$ are zero for $n<0$. Then we have $$\nu'_k(n) = a_1(n,k) + a_1(n-1,k),$$ where the terms enumerate $v$ starting with 0 and 1, respectively. The count $a_1$ satisfies the recurrence: \begin{split} a_1(n,k) &= [k=1] + a_1(n-2,k) \\ &+ \sum_{p=2}^{2k-1} \sum_{k_2 = \lceil k/(1+c_p)\rceil}^{\lfloor (k-1)/c_p\rfloor} a_2(n-1-p,k-c_pk_2,k_2), \end{split} where $p$ runs over the possible lengths of the initial run of 0's in $v$, the first term corresponds to $v=0^n$ and the second term corresponds to $p=1$, and $c_p:=\left\lfloor\frac{p}2\right\rfloor$. Finally, the count $a_2$ satisfies the recurrence: \begin{split} &a_2(n,k_1,k_2) = [(k_1,k_2)=(1,1)] \\ &+ [k_1=k_2]\cdot\sum_{c=1}^{k_1-1} \sum_{t = \lceil k_1/(1+c)\rceil}^{\lfloor (k_1-1)/c\rfloor} a_2(n-1-2c,k_1-ct,t) \\ & + [k_1<k_2]\cdot a_2(n-1-(2\lfloor \tfrac{k_1-1}{k_2-k_1}\rfloor+1), (k_1-1) \bmod (k_2-k_1) + 1,k_2-k_1), \end{split} where the terms correspond to $v=0^n$, even $p>0$, and odd $p>0$, respectively.
Example $k=1$. In this case we have $a(n,1) = 1 + a_1(n-2,1)$, implying that $a_1(n,1)=1+\left\lfloor\frac{n}2\right\rfloor$. Then $a_2(n,0,1) = 0$ and $a_2(n,1,1) = 1$. It follows that $\nu'_1(n) = n+1$ and $\nu_1(n) = 2n$.
ADDED. It can be seen that $a_2(n,k_1,k_2)$ stabilizes as $n$ grows and its limit $\bar a_2(k_1,k_2)$ satisfies the recurrence: \begin{split} &\bar a_2(k_1,k_2) = [(k_1,k_2)=(1,1)] \\ &+ [k_1=k_2]\cdot \sum_{c=1}^{k_1-1} \sum_{t = \lceil k_1/(1+c)\rceil}^{\lfloor (k_1-1)/c\rfloor} \bar a_2(k_1-ct,t) \\ & + [k_1<k_2]\cdot \bar a_2( (k_1-1) \bmod (k_2-k_1) + 1, k_2-k_1). \end{split} Then it is easy to find the coefficient $q_k$ of $n$ in the linear formula for $\nu_k(n)$ (which is the quadruple of such coefficient in $a_1(n,k)$) as $$q_k = 2[k=1] + 4\sum_{c=1}^{k-1} \sum_{k_2 = \lceil k/(1+c)\rceil}^{\lfloor (k-1)/c\rfloor} \bar a_2(k-ck_2,k_2).$$ Here are the values of $q_k$ for $k\leq 30$:
2, 4, 8, 12, 16, 24, 24, 36, 40, 48, 40, 88, 48, 72, 96, 108, 64, 152, 72, 176, 144, 120, 88, 312, 144, 144, 200, 264, 112, 416
There seems to be no easier way to get the free term of $\nu_k(n)$ than computing it as $\nu_k(n) - q_kn$ for large enough $n$.