@Adeek unfortunately i'm not quite sure too! i suspect that things might be easier if the original thing was written in the language of schemes... (or maybe not)
anyway - I think the idea is that, say you have a variety defined over $k \isom \mathbb{Q}(T)$ (e.g. if it is defined over $\mathbb{Q}(\pi)$, then if you think about the transcendental points on $\mathbb{P}^1$, these would correspond to different embeddings of $\mathbb{Q}(T)$ to $\mathbb{C}$,
so if you're only thinking of the transcendental points, then at least it seems "right" to me that thinking this way gives you some notion …