In many cases, because both overlap with geographical features: the Carpathians in Romania, the Pontic-Caspian steppe in Ukraine, the green mountainous Portugal north of the Tagus vs the flat "montado" landscape to the south.
It's easy to see why old empires/countries were divided by geographical features due to military reasons. But why would it affect the current-day political climate directly?
I think the causal relation is more like
Geo -> old empire -> (more things) -> current day politics
Geo -> old empire
Geo -> current day politics
Edit: on a second thought, I think a factor that supports your point is that geographical feature would affect corresponding industries in certain area regardless of "historical divisions". Maybe this is what you mean?
geography → economy → old empire
geography → economy → current day politics
geography + current tech → agriculture/commerce/industry/military → economy/culture → politics
When you said geography features, I was more thinking of natural barrier (like rivers, mountains): they were very crucial in shaping the old country border, but should have less impact today if both sides are already in the same country. So it's interesting that some of political division are still present around them, which makes me think history has its (unproportional) influence than the geography itself. But I guess it's always multi-factor and hard to tell in vacuum.
It doesn't help that in most of examples in OP, the major difference between two (old) countries is the economic one, so a certain degree of Matthew effect is there.