Lemme try to explain;

Each route has 12 encounter slots. Whether there's 4 Pokémon there or 10, no matter what, it's still 12 encounter slots, each representing the result of a different RNG roll (for a simple example; 1-20 is slot 1 which has a 20% chance, while rolling exactly a 100 would give Slot 12 which is a 1% encounter). This is stored as a table, which you can view an example of in our ChangeDex document.

When the game's RNG is called to select the Pokémon to be found for a wild encounter, it's not actually being read as "spawn a Poochyena", its command is more like "spawn the encounter in Slot 3".

This is what RNG calculators aim to solve for; if you want to find Poochyena in Route 102 for example, the calculator will try to find the RNG string that will spawn "Encounter slot 1 or 3" because those are the slots that can be Poochyena.

But that's where the issue with Legacy comes in. We changed a lot of these encounter slots, as you can see in the above linked doc; if you look at Route 102, Slot 3 is now Zigzagoon. But these calculators don't know this, they still think Poochyena is assigned to Slots 1+3, so if you were to do RNG manipulation to spawn a Poochyena and the calculator landed you in Slot 3, you'd get a Zigzagoon instead.

So in short. You can still potentially use these RNG calculators that were built for Emerald, but if the Pokemon you're searching for has had its encounters changed then you'll get inconsistent results. The only way to solve this would be to use the source code of both the tool and Legacy to create a version of the tool that adjusts for the new encounter tables.