Now that the Code Jam Qualifiers are over, I'll post a full solution.
First, we know that the minimum possible area is $1$, which is the area of a single face. The maximal area is $\sqrt{3}$, which is given in the problem as the upper limit for full points $-$ written as the inequality $1.000000<A<1.732050$. You can also see why this is the maximum by checking out the answer G Cab provided.
First, we'll need a way to calculate the area of a projected cube as a function of it's normal vectors. We let $n_1=(n_{11},n_{12},n_{13}),n_2=(n_{21},n_{22},n_{23}),n_3=(n_{31},n_{32},n_{33})$ be the vectors pointing from the center of the cube to the center point of 3 nonparallel faces, and $n_p = (0,1,0)$ be the normal vector of the plane. Then, if $\phi_i$ is the angle between $n_i$ and $n_p$, the area of the projection is $A = \sum_{i=1}^3 |\cos\phi_i|$. We can calculate $|\cos\phi_i| =\left|\frac{n_i\cdot n_p}{|n_i||n_p|}\right| = 2|n_{i2}|$, since $|n_i|=\frac{1}{2}$. This gives us the formula for the area $A = 2\sum_{i=1}^3 |n_{i2}| = 2|n_{12}|+2|n_{22}|+2|n_{32}|$.
Next, we need to find a configuration which gives the minimum possible area and one which gives the maximum. The minimum area is easy, as it's the default state of the cube. If we write the coordinates as a matrix $N = (n_{ij})$, we can see that a minimal configuration is
$\frac{1}{2}I_3 = \begin{bmatrix}1/2&0&0\\ 0&1/2&0\\ 0&0&1/2\end{bmatrix}$,
and the area is twice the sum of the second row: $A = 2(0+1/2+0) = 1$. A maximal configuration can be found when the long diagonal of the cube (from bottom left front to top right back) is parallel to $n_p$. To show this, we will look at it from a different coordinate system, where the cube is aligned with the axes, with normal vectors $m_i=\frac{1}{2}e_i$, and the plane normal vector is
$m_p = \left(\frac{1}{\sqrt{3}},\frac{1}{\sqrt{3}},\frac{1}{\sqrt{3}}\right)$. This this configuration, the cosine of the angles between the cube normals and plane normal are $\cos\theta_i = \frac{1}{\sqrt{3}}$, so the area is $A=\sqrt{3}$, which is known to be the maximum.
So, now that we have a minimum configuration and a maximum configuration, if we can generate a continuous function between these two orientations, then Intermediate Value Theorem will guarantee that there's a solution to the function for any possible $A$. To do this, we take an axis of rotation to be the line $x=z, y=0$, which is written as $(\frac{1}{\sqrt{2}},0,\frac{1}{\sqrt{2}})$ in vector form. Let $\psi$ be the angle in radians rotated about this axis from the starting minimal configuration. Then, $A = f(\psi)$ has $f(0) = 1$. Further, if we rotate by some amount $\psi_m$, we will reach the maximal configuration, so $f(\psi_m) = \sqrt{3}$.
To calculate $f(\psi)$, we use the same formula for calculating the area of the projection, but we multiply each of the $n_i$ by the corresponding rotation matrix $R = \begin{bmatrix}\frac{1+\cos\psi}{2} & -\frac{\sin\psi}{\sqrt{2}} & \frac{1-\cos\psi}{2}\\ \frac{\sin\psi}{\sqrt{2}} & \cos\psi & -\frac{\sin\psi}{\sqrt{2}} \\ \frac{1-\cos\psi}{2} & -\frac{\sin\psi}{\sqrt{2}} & \frac{1+\cos\psi}{2} \end{bmatrix} $.
This gives $N = R(\frac{1}{2}I_3) = \frac{1}{2}R$, and summing the absolute values of the second row gives the area as $A = |\cos\psi|+\sqrt{2}|\sin\psi|$. For $0 < \psi < \pi/2$, we can drop the absolute values, so that $A = f(\psi) = \cos\psi + \sqrt{2}\sin\psi$. This function takes it's first maximum at $\psi_m = 2\tan^{-1}\left(\frac{\sqrt{2}}{1+\sqrt{3}}\right) \approx 0.95532 < \pi/2$. So, for a given $A$, we can find $\psi_A = 2\tan^{-1}\left(\frac{\sqrt{2}-\sqrt{3-A^2}}{1+A}\right)$. This gives us (with a little bit of trigonometry) $\cos\psi = \frac{1}{3}(A+\sqrt{2}\sqrt{3-A^2})$ and $\sin\psi = \frac{1}{3}(\sqrt{2}A-\sqrt{3-A^2})$.
Last, all we need to do is substitute these values into the matrix $N$ to get the final answer:
$N = \begin{bmatrix}\frac{1}{12}(3+A+\sqrt{6-2A^2}) & \frac{1}{12}(-2A+\sqrt{6-2A^2}) & \frac{1}{12}(3-A-\sqrt{6-2A^2}) \\ \frac{1}{12}(2A-\sqrt{6-2A^2}) & \frac{1}{6}(A+\sqrt{6-2A^2})
& \frac{1}{12}(-2A+\sqrt{6-2A^2}) \\ \frac{1}{12}(3-A-\sqrt{6-2A^2}) & \frac{1}{12}(2A-\sqrt{6-2A^2}) & \frac{1}{12}(3+A+\sqrt{6-2A^2}) \end{bmatrix}$,
where the columns are the coordinates of the points in the center of 3 nonparallel faces.