Technically, the link element is not a meta tag, so it wouldn't apply to that :). In practice, it's a bit more complicated. We don't use the link-alternate-hreflang construct for geotargeting in that it doesn't promote local results (like normal geotargeting might). However, the ultimate effect is somewhat similar, since we use it to swap out the best match from a list of alternatives should any one of them show up in search results.
With regards to the soft-404s/duplicate-content-URLs, the final result is very similar and depends a bit on the URLs that we find on your site. If we see a large number of them showing the contents of the homepage (or even redirecting to it), we would probably assume that's a soft-404 and focus on the homepage. If we see a handful of them showing the same content - and perhaps other URLs on the site showing normal 404 errors - then we might see that as duplicate content, which we'd try to combine with the homepage. In both situations, we'll try to focus on the homepage once our algorithms determine that these alternatives do not need to be indexed separately.