As far as Google is concerned, I don't think they will care about a meta-refresh on the 404 page. Googlebot can still tell which pages are not found. If a meta-refresh is a better user experience than showing a generic 404 page, then there shouldn't be too much wrong with it.
That being said, I can't imagine that refreshing the page of users is as good as showing a truly helpful 404 page right off the bat. Why redirect to the home page, when you could put home page content right on a custom 404 page and save visitors the hassle of the refresh?
I also find that it is usually worth paying lots of attention to 404s on your website. I correct all incoming broken links using 301 redirects. I also try to run the url through site search and redirect based on the first result. So example.com/keyword will redirect to the actual url example.com/article?id=4.
I highly doubt that what these websites are doing with their 404 pages is contributing to their rankings much, but I would recommend paying attention to your 404s to keep your users happy.