It completely ignores the influence of the indigenous languages in the "dialect" or variation of Spanish, which is actually a much better explainer than "distance from spain".
Huge mountain ranges separating people that are close in distance is a pretty classic mechanism of creating linguistic diversity / dialects in places that are physically close to each other. You see this with villages in various parts of Asia historically.
Indigenous language effecting Spanish is something that would effect everyone in South America, so even if you remove Spain from the table, Colombia, Chile, the Caribbean and Costa Rica will all stand out about how "different" they are from the rest of South America, probably from their physical barriers separating them from the rest of the continent.
I don't think that's a good hypothesis, because in that case, other countries with a huge colonized population such as Mexico or Perú would have less intelligible dialects as well.
Not all Latin-American countries experienced the same level of mestizaje and colonization. The southern part of Chile, in particular, was never successfully colonized by the Spaniards, and mapudungún, the language of the Mapuche people who live there has had (and continues to have) a tremendous influence on Chilean Spanish.
