But that's besides the point. That they're greenhouse gases doesn't really figure into the reason why it's EU policy to reduce the density of their emissions near natura 2000 areas.

Correct, but in the Netherlands the problem is that they're killing our existing flora and fauna. Especially in areas where nature reserves and farming are close together, this causes issues. The Netherlands is the 2nd biggest food exporter in the world, after the US. But we're only the 134th largest by land mass and 69th largest by population.

The amount of farming we do in our tiny country is pushing the limit of what you can do to nature and it's causing issues on a local scale. The unfortunate thing is that we're about the most efficient producer in the world too, so on a global scale, cutting down production here would probably be a bad thing.

That have a short life at the atmosphere.

They are relevant for local warming (normally named "heat islands"), but not much for global warming. Anyway, they have much more important local effects, so mostly nobody cares about the warming.