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".
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.