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The reason rubocop stops and asks the user to remove rubocop-todo.yml from the configuration is that it can't have configuration settings from the old todo file active while it's generating the new one. Because that would produce a rubocop-todo.yml containing only the offenses not disabled in the old one.
A better solution is probably to just skip all rubocop-todo.yml files while reading configuration when --auto-gen-config is given. It would overwrite an existing rubocop-todo.yml without asking, but I think that's no big issue.
When a .rubocop.yml occurs in a parent directory, it is not used, I believe. Rather, it uses the .rubocop.yml in the child directory.
However, --auto-gen reaches up into the parent directories to find a reference to ruboocp-todo.yml, and complains (incorrectly):
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