It appears I was reading the question wrong, and it wanted to calculate the sample mean & variance, not variance related to discrete random variables.
Since $N= \sum _{r = 0}^{2n-1} \beta_r = 2^n$, we already have $\mu = \frac{2^n}{2n}$.
To calculate sample variance, use the formula:
$$\sigma^2 = \frac{1}{2n} \sum_r {(\beta_r - \mu)^2} = \frac{1}{2n}\left(\sum_r \beta_r^2\right) -\mu^2 \tag{1}$$
To calculate the first term, note that if we let:
$$ \textbf{x} = \left( 2^{2^\alpha \gcd(1,n'')}, 2^{2^\alpha \gcd(2,n'')}, ..., 2^{2^\alpha \gcd(n,n'')} \right)$$
$$f_t = \frac{1}{\sqrt{n''}}\left( e^{2\pi i \frac{t}{n''}}, e^{4\pi i \frac{t}{n''}}, ..., e^{2n''\pi i \frac{t}{n''}} \right)$$
So that:$$\beta_r = \frac{\sqrt{n''}}{2n}\langle \mathbf{x}, f_r \rangle$$
Then $\{ f_0, f_1, ..., f_{n'' - 1} \}$ forms an orthonormal basis in $\mathbb{C}^{n''}$ with the standard inner product. Using Parseval's identity for Hilbert spaces:
$$\begin{align}\sum_{r=0}^{n'' - 1} \beta_r ^2 &= \sum_{r=0}^{n'' - 1} |\beta_r|^2 \\ &= \frac{n''}{4n^2}\sum_{r=0}^{n'' - 1} |\langle \mathbf{x}, f_r \rangle|^2 = \frac{n''}{4n^2}\langle \mathbf{x}, \mathbf{x} \rangle \\ &= \frac{n''}{4n^2}\sum _{j=1}^{n''}\left( 2^{2^\alpha \gcd(j, n'') } \right)^2 \end{align}$$
And note that from the first term in $(1)$, we use the fact that $cn'' + r \equiv r \mod n''$ given $r = 0, ..., n'' - 1$:
$$\sum_{r=0}^{2^{\alpha + 1}n''-1} \beta_r^2 = \sum_{c=0}^{2^{\alpha +1} -
1}\sum_{r=0}^{n''-1} \beta_{cn'' + r}^2 = \sum_{c=0}^{2^{\alpha +1} -
1}\sum_{r=0}^{n''-1} \beta_{r}^2 = 2^{\alpha +1}\sum_{r=0}^{n''-1} \beta_{r}^2$$
Putting these together, we have:
$$\begin{align} \sigma^2 &= \frac{1}{4n^2}\sum _{j=1}^{n''}\left( 2^{2^\alpha \gcd(j, n'') } \right)^2 - \frac{2^{2n}}{4n^2} \\ &= \frac{1}{4n^2}\sum _{j=1}^{n'' -1}\left( 2^{2^\alpha \gcd(j, n'') } \right)^2 \tag{2} \end{align}$$
For the second part of the question, using an inequality for sums of squares and another inequality yields:
$$\frac{1}{n'' - 1} (\beta_0 - \mu)^2 \leq \sigma^2 \leq (\beta_0 - \mu)^2$$
Note that $\beta_0 / \mu \approx 1$, especially for large $n$:
$$
\begin{align}
\frac{\beta_0}{\mu} &= \sum_{j=1}^{n''} 2^{2^\alpha (\gcd(j,n'') - n'')} \\
&= 1 + \sum_{j=1}^{n'' - 1} 2^{2^\alpha (\gcd(j,n'') - n'')} \\
&\leq 1 + \sum_{j=1}^{n'' - 1} 2^{2^\alpha (\frac{n''}{3} - n'')} \tag{3} \\
&= 1 +(n''-1){2^{-2n/3}} \approx 1
\end{align}
$$
In $(3)$, use the fact that $\gcd(j,n'') \neq n''$ if $j = 1,...,n''-1$ and so the next largest value (assuming $n''>1$ and odd) is $\gcd(j,n'') \leq n''/3$. Note the above inequality remains true even if $n'' = 1$.
And in the other direction:
$$
\begin{align}
\frac{\beta_0}{\mu} &= 1 + \sum_{j=1}^{n''-1} 2^{2^\alpha (\gcd(j,n'')-n'')} \\
&\geq 1 + \sum_{j=1}^{n'' - 1} 2^{2^\alpha (-n'')} \\
&= 1 +(n''-1){2^{-n}} \approx 1
\end{align}
$$
Also, $\beta_0/\mu \leq 1.5$. So in relative magnitude, $\beta_0 \approx \mu$ as $n$ increases and in this respect, the variance is small in this relative sense (although not in absolute sense).