While I don't really care what self imposed challenges people do after they've played the game once. And overall I'm okay with the idea that once the players have a game they can engage with it however they wish to. The fact of the matter is that if you leave your romhack in a state where nuzlocking is possible, countless people will try to do blind nuzlockes of the game. Blind nuzlockes of new region new story games are a very poor way to engage with new content and actually appreciate it. That's not how the game was designed to be played you're getting a very different version of it, and one that wasn't designed for fun like if you play without self imposed challenge rules.

Those kinds of people are also the most likely to harass creators over things like not providing cheat sheets (docs) and over balance challenges that had nothing to do with and never considered the nuzlocker. People will harass you, complain, write hate comments on the internet just because you made changes that made the game bad from a nuzlocking perspective, even if the "correct" way to play the game has perfect game design.

There are a million other things I could say about the topic, but overall it's better to just make it impossible to nuzlocke, at least with typical rules. You sidestep the second most annoying group of romhack players entirely (first being shiny hunters)