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...?
More than a special status as a host country, as far as I understand it is explicitly not a member state, hence it's separated from the rest of the flags (Which is curious because despite being the host country, it doesn't guarantee you being a member state of ESO).
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/