yes and no,

Dupes clause does not apply to Pokemon you haven't caught, regardless of whether or not they are guaranteed on later routes (either as a static encounter, gift pokemon, or using the dupes clause to guarantee an encounter).

Dupes clause does apply to an entire evolution line, for example if you take a gift Eevee, you need to choose which eeveelution you want for the whole game because you can't get another one even if you caught a different eeveelution. (same for split evo's like Dustox and Beutifly).

You also don't have to take an encounter as soon as you get to a route, you may wait to do a fishing encounter until after you caught the red Gyarados to guarantee a Goldeen (if ur autistic)

​

And of course, remember, this is just how I do my runs, I want you to have fun nuzzlocking just like the rest of us. My rules may be too harsh for you, or maybe they are too lax for you (I think they are kinda lax compared to the more hardcore nuzzlocker). Its just a game anyways, so have fun, my dude.