@Luigi Based on the error you’ve mentioned it sounds like you’re trying to literally add the domain as the Custom Domain for two separate site instances in Netlify.
That isn’t possible, nor is it what the article you’ve linked to says can be done.
The main instruction in the article is this one:
The idea is that you set up a site instance which does have the custom domain against it, along with other separate site instances, and then against the main site you configure proxies that point to the other sites and mimic subfolders.
So that when a user visits content at /v2 for example, they end up seeing whatever you have hosted on https://yourotherrepository.netlify.app/.
Does that make sense?