This is because of the fact that APC's are flat fees (usually given in US dollars, british pounds and euros only) and therefore there is no regional pricing. Most online markets have diffferent prices, for instance video games on steam are often much cheaper in brazil, for instance looking at battlefield 6's price on steam it is £40 in brazil but £60 in the UK [1]. Nature communications for instance has an APC of £5290, or $7k. This is 4 months of salary for a post doc in brazil, but only one and a half months in the UK. Given the number of articles submitted by brazillan researchers is much lower than from north america, europe and china it makes sense for the journals to simply waive fees for these countries, as opposed to keeping up with currency conversion and purchasing parity. It is usually relatively easy to use the waivers also.

Note the maths becomes substantially worse when you look at poorer countries than brazil.

[1]: https://steamdb.info/app/2807960/