Decisions on whether or something is duplicate is usually made mostly on the title of the question. If the question is really not duplicate, the best way to get it re-opened is to edit it and differentiate the title. You would also want to link to the duplicate and explain why the answers to it might not apply. Once a question is edited, it automatically enters the re-open queue and users on the site can vote on whether or not they think it is duplicate.
I'd say that posting in meta asking whether a specific question is duplicate or not is not appropriate. Getting a question into the re-open queue should be a good enough mechanism that we shouldn't need lots of meta questions about individual posts.
That being said, if there is a pattern of questions closed for dubious reasons, meta would absolutely be place to discuss.
So if you want the question re-opened I would edit the title to say:
Remove a site from Google search once it has been retired and shut down
And add a paragraph to the body:
Removing full site from Google index has been discussed as a possible duplicate but the answers there show what to do with a site that still exists. Once the site is shut down, those mechanisms such as robots.txt won't be available.