If you are mistreated in your country, why does it matter if you are a member of an underrepresented group or not?
In what countries are over-represented groups mistreated by systems or institutions?
To me (and, I suspect, to Gitlab), "underrepresented" means "present in lower proportions than in the general population".
South Africa, to use one of your examples, has a majority Black African population (80%), but business management is overwhelmingly White[1] (67%).
That means Black African people are simultaneously the majority of the country and also underrepresented minorities that struggle with systemic, institutional racism.
I think it does matter whether you're a member of a group that is mistreated as a group vs. whether you are mistreated as a person; it's easier to be confident that you're understanding the situation correctly if there's a lot of data about an entire group vs. a claim that you individually are unsafe/mistreated (which could just be "I am mistreated because my community is ostracizing me for having committed a crime" or whatever). It is obviously possible to be mistreated as a group even if you are from a local-majority group (cf. apartheid in South Africa).
As to why they mentioned it even if it's in parentheses - there's a link to a page, and elsewhere on the page they mention that it's a cultural value to include more people from "underrepresented groups" in their definition (https://about.gitlab.com/company/culture/inclusion/#gitlabs-...).