I believe such organisations tend to do such things very intentionally :-)

About ESO [1]

> We are an intergovernmental organisation established in 1962 supported by 16 Member States (Austria, Belgium, Czechia, Denmark, Finland, France, Germany, Ireland, Italy, the Netherlands, Poland, Portugal, Spain, Sweden, Switzerland and the United Kingdom), our host country Chile and strategic partners.

So Chile has a distinct status, hence the margin...?

[1]: https://www.eso.org/public/about-eso/

The flags have also all (except for Finland, which appears slightly wider?) been squeezed into a uniform 3:2 aspect ratio; some of them (e.g. Belgium, Switzerland, United Kingdom) properly ought to have different proportions. I understand they can look more aesthetically pleasing when they’re all the same size, but it’s another little detail to notice. :-)

Now I can't unsee it :/