The transclusion between wikis (using templates like iwpage) is not managed by the ProofreadPage extension. So, it shouldn't be fixed by the extension, as long as the support of interwiki transclusion is not added to it (and I believe it won't as long as there are no clean ways to do such things).

I think it should be done in https://wikisource.org/wiki/MediaWiki:InterWikiTransclusion.js that is the current backend for {{iwpage}}

Contents is transcluded through javascript, I'm unsure if google is able to index it. There is a lot of uncertainty about what google and other SE do with javascript. Some content created by js are indexed, some other aren't, some SE doesn't support at all any javascript. Anyway even on it.wikisource.org the following request doesn't return the right Page:

site:it.wikisource.org "misurando a passi tardi"

Are all Page: on it blocked from indexing through their robots.txt ?

As pointed by Tpt, this can't be solved without a clean transwiki transclusion and it'll remain the problem of the canonical <link.