I'll consider the modified version of the problem where all sets are centrally symmetric (i.e., $K=-K$, $E=-E$), and show that in this case the answer to question (a) is **NO**. It seems obvious that the same counterexample below should also answer negatively the original question, but I haven't tried to prove this. The counterexample roughly follows the idea suggested by Gerhard Paseman.

I'll normalize all areas to $\pi$ instead of $1$.

Let $\varepsilon$ be a fixed parameter in the interval $(0,1/9]$.
Let $K$ be the topological disk bounded by the Jordan curve given in polar coordinates by:
$$
r^2 = 1 + \varepsilon \cos 4 \theta .
$$
The figure shows the case $\varepsilon = 1/9$:
[![my convex set][1]][1]

I claim that **$K$ is a counterexample**, i.e., there are at least two different ellipses $E$ of area $\pi$ that minimize the area of $K \vartriangle E$.

Proof of the claim: Obviously, $K$ has area $\frac{1}{2}\int_0^{2\pi}r^2 d\theta = \pi$.
Convexity is a calculus exercise. 

Note that $K_\varepsilon$ is invariant under $R_{\pi/2}$ (the rotation of $\pi/2$).
Therefore if $E$ is a minimizing ellipse, so is $R_{\pi/2}(E)$.
So, to prove that the minimizing ellipse is not unique, it is sufficient to show that the unit disk is not a minimizer. 

Let $t$ be a real parameter and let $E_t$ be the ellipse with boundary $e^{t} x^2 + e^{-t}y^2 = 1$, or in polar coordinates
$$
r^2 = \frac{1}{e^t \cos^2\theta + e^{-t} \sin^2\theta} =: f(\theta,t).
$$
Note that $R_{\pi/2}(E_t) = E_{-t}$, and so the function $A(t) := \mathrm{area}(K \vartriangle E_t)$ is even.


Let $g(\theta):= 1+\cos 4\theta$ and $h(\theta,t) := f(\theta,t) - g(\theta)$.
For $t$ sufficiently close to zero, 
the function $\theta \mapsto h(\theta,t)$ has two roots in the interval $[0,\pi/2]$, say $\alpha(t) < \beta(t)$.
Then
$$
A(t) = 2 \, \mathrm{area}(E_t \smallsetminus K) = 
8 \int^{\beta(t)}_{\alpha(t)} h(\theta,t) d\theta .
$$
By the Leibniz integral rule,
$$
\frac{1}{8} A'(t) = \int^{\beta(t)}_{\alpha(t)} h_t(\theta,t) d\theta +  \underbrace{h(\beta(t),t)}_{0} \beta'(t)- \underbrace{h(\alpha(t),t)}_{0} \alpha'(t)
$$
and 
$$
\frac{1}{8} A''(t) = \int^{\beta(t)}_{\alpha(t)} h_{tt}(\theta,t) d\theta + h_t(\beta(t),t) \beta'(t) - h_t(\alpha(t),t) \alpha'(t) .
$$
Substituting $t=0$ and using the Implicit Function Theorem,
$$
\frac{1}{8} A''(0) = \int_{\pi/8}^{3\pi/8} h_{tt}(\theta,0) d\theta - \frac{[h_t(3\pi/8,0)]^2}{h_\theta(3\pi/8,0)} + \frac{[h_t(\pi/8,0)]^2}{h_\theta(\pi/8,0)}.
$$
Some calculations show that:
$$
h_t(\theta,0) = -\cos 2\theta, \quad 
h_{tt}(\theta,0) = \cos 4\theta, \quad 
h_{\theta}(\theta,0) = 4 \varepsilon \sin 4\theta.
$$
Substituting we get:
$$
\frac{1}{8} A''(0) =  \int_{\pi/8}^{3\pi/8} \cos 4\theta d\theta - \frac{[1/\sqrt{2}]^2}{4\varepsilon \times 1} + \frac{[-1/\sqrt{2}]^2}{4\varepsilon \times (-1)} = -\frac{1}{2}.
$$
In particular, $A''(0) < 0$.
Since the function $A$ is even, we conclude that $t=0$ is a local maximum. 
So the unit disk is not a minimizer for the area of the symmetric difference.
As explained before, symmetry allows us to conclude that the minimizing ellipse is not unique.

**Remark:** The minimizer ellipses seem to be **very** close to the unit circle. Here is a plot of the area $A(t)$ for $\varepsilon=1/9$:
[![Graph of area function][2]][2]
There is no discontinuity. Non-differentiability occurs when $E_t$ and $K$ have tangencies. 

  [1]: https://i.sstatic.net/6bVzw.jpg
  [2]: https://i.sstatic.net/o7qlF.jpg