Defining the observation matrix for a Linear Kalman Filter
The first question you link to states that it only measures acceleration and the answer suggests to add the acceleration to the state vector as well, $\begin{bmatrix}x^\top&amp;\dot{x}^\top&amp;\ddot{x}^\top\end{bmatrix}^\top$. This is why the observation matrix becomes $\begin{bmatrix}0&amp;0&amp;I\end{bmatrix}$.

So your reasoning for observation matrix is correct. I only have one remark, namely it is given that the drone moves in 3D space, so the observation matrix should actually be

$$
\begin{bmatrix}
I&amp;0\\0&amp;I
\end{bmatrix}
$$

with $I$ a three by three identity matrix. So effectively the observation matrix would be a six by six identity matrix.