Question: "Why should we prefer that? The professor mentioned that was because we want to avoid "weird" automorphism of k. I couldn't understand what he was trying to explain by that. Could anyone explain this a bit more details? Some concrete example would be great. Thank you!"
Answer: Any pair of schemes $X,Y$ have canonical maps to $S:=Spec(\mathbb{Z})$ and any map
$f: X\rightarrow Y$ is defined over $S$. Hence you may view an arbitry map of schemes as maps over the integers $\mathbb{Z}$. When working over a field $k$ you change your base scheme $S$ to $T:=Spec(k)$. There is a canonical map $\phi: \mathbb{Z}\rightarrow k$ mapping $\phi(m)=\phi(1+ \cdots + 1)=m\phi(1)=m\in k$. Hence the map $X \rightarrow S$ factors canonically as $X \rightarrow T \rightarrow S$. Hence when you are not working over a field $k$ you are working over $\mathbb{Z}$.
Example 1: If $k:=\mathbb{Q} \subseteq K:=\mathbb{Q}(i)$ you may look at two groups:
$$End_k(K)\text{ and }End_K(K).$$
Since $dim_k(K)=2$ it follows $End_k(K)=Mat(2,k)$ is the ring of $2\times 2$-matrices with coefficients in $k$ and $End_K(K)\cong K\cong k^2$. Hence when you change base field the situation changes.
Example 2: A map $\phi^*: Spec(K) \rightarrow Spec(K)$ defined over $k$
is given by an automorphism $\phi \in G(K/k)$ and there is only one map defined over $K$ - the identity map. The Galois group $G(K/k)$ enters in various formulas in algebraic number theory and arithmetic geometry, and when you change the base field, the set of morphisms changes and this relates to the Galois group.
Example 3: If $V\cong \mathbb{k}^{n+1}$ is a vector space over a field $k:=\mathbb{k}$, it follows there is a 1-1 correspondence between maps (over $k$)
$$ x: Spec(k) \rightarrow \mathbb{P}(V^*)$$
and lines $l_{x} \subseteq V$. Hence the $k$-rational points $x \in \mathbb{P}(V^*)(k)$ correspond 1-1 to lines $l_x \subseteq V$. This reflects the fact that projective space $\mathbb{P}(V^*)$ is a parameter space - it parametrize lines in $V$.