I may be wrong, but it looks like the plugin is for when you're moving your blog from one domain to another. i.e. It will have all of the old content in the same site structure, plus added new posts/pages.
And I again may be wrong, but it looks like the search bots will need to hit each and every URL of the old site to get the "moved permanently" message.
Over the years I have removed some pages and given them "moved" and "gone" headers. Yet even now some of those pages get called. Months and even years for some bots. I guess there are pages with links to them and the bots find them that way. Still, I wish they'd get the message and remember it!
So I think if it was me I'd keep the old domain and simply redirect every request to it to the new domain using a simple htaccess file. That way if the same relative path exists, fine. If it doesn't you could send them to the index, sitemap or search page.