Overlaping of Wild Encounters from Modern Emerald and Vanilla in the Pokédex

[resetes12]

Wild encounters in the Pokédex overlap and I cannot find a reliable way of handling two different encounter tables (actually 4, 2 for Vanilla day and night, and 2 for Modern day and night).

Example:
You can catch Nidoran if you have Modern Spawns enabled in Route 116, but you can't with Vanilla Encounters. If you somehow get Nidoran with Vanilla Encounters, Nidoran will show up in the Pokédex in Route 116 even if it's not really there. Both encounter tables overlap.

Current solution:
Using the code used for hiding Wynaut in Route 130, all Pokémon not available in Vanilla Emerald are hidden the same way. It mostly works, however, certain Pokémon like Houndour which can be found earlier and in different routes compared to Vanilla Emerald when using the new encounters will show up in the Pokédex with Vanilla encounters even if they are not available there. It's a working solution but not the one I want.

I'm asking for some help solving this small, nitpicky issue. Any help, information, or ideas are welcome.

[resetes12]

You can see the current solution in pokedex_area_screen.c (sSpeciesHiddenFromAreaScreenModern)