And something similar to how you manage the La Paz / Sucre thing might need to be also worked out for Cape Town / Bloemfontein / Pretoria. Otherwise, another fun quiz!
The way you've dealt with South Africa only created a bigger mess. Now South Africa is represented by two capitals, unlike all other countries. What's more, the order of the African capitals is confusing. Although both Cape Town and Bloemfontein are further south than some others, they're put at the bottom of the list.
I personally like the fact that South Africa's capitals are included separately, and the title of the quiz does allow for this, but there really, really should be a caveat about it, or it's quite annoying.