Why do nidoran evolve differently based on gender, but other pokemon which experience relatively extreme gender dimorphism (such as frillish) become the same pokemon no matter what their gender? What sets nidoran apart?

Strangely, the nidoran lines are the only pokémon lines whose male and female counterparts … are not the same species. That is, although the two get along well enough, they’re about as similar to one another as plusle are to minun. The only reason they’re both called nidoran is because they look like one another, often form mated pairs (even if the advanced stages can’t breed), and live in the same burrows, so scientists mistook them for the same species with a divergent evolution tree (much like the burmy line) until later studies revealed that they’re only related, not the same.

So that should answer the question about their evolution lines: they are, quite simply, actually two separate lines from their base onwards.