Friedmann equation states
$$ H^2 \equiv \left( \frac{\dot{a}}{a} \right) = \frac{8\pi G \rho}{3} - \frac{k}{a^2} $$
which describes the evolution of the expansion of the universe. Writing $\Omega(t) = \frac{8 \pi G}{3 H^2(t)}\rho(t)$ we get
$$ |\Omega(t) - 1| = \frac{|k|}{a^2H^2}.$$
Which in a radiation or matter dominated universe gives
$$ |\Omega(t) - 1| \propto t^n, \quad n\geq 2/3.$$
Thus, if the universe is flat now, it was a lot flatter right after the big bang. This is called the flatness problem, but I am having a hard time understanding why it is a problem.
My way of thinking is this: The topology of a closed (open) universe and a flat universe are very different. If the universe is flat ($k=0$) then the spatial part of universe has the topology of $\mathbb{R}^3$, but the topology of a closed universe is a 3-sphere $S^3$. Now, since we have good reasons to think that our universe is pretty flat, why is that not an argument for the universe being exactly flat? As in exactly $k=0$. If $k$ was shown to be exactly $k=10^{-100}$, I understand that we would have a fine-tuning problem. But since the topology of the entire universe would be profoundly different going from being a non-compact $\mathbb{R}^3$ ($k=0$) to being a compact 3-sphere $S^3$ ($k=10^{-100}$), I can easily accept that $k=0$ is a possibility.
Why do physicist think that $k=0$ is unrealistic? Where am I wrong? Have I misunderstood something? Please correct me if I am wrong about something.