According to the official documentation you should be able to associate a scope with a registry when logging in. Is this what you want?
Did you try the following?
npm login --registry=https://reg.example.com --scope=@myco
If you dont want to login, but rather want to specify the token explicitly, the following should work:
npm config set @myco:registry https://reg.example.com
npm config set //reg.example.com/:_authToken xxxxxxxx
Note that the registry url must be normalized for this to work, ie it shouldn’t include scheme and must end with a slash.