Comment by Sophira

Sites that exist to archive other websites will almost always need to dynamically change the content of the HTML that they're serving in some way or another. (For example, a link that points to the root of the website may need changed in order to point to the right location.)

So it doesn't necessarily raise questions about whether the content has been changed or not. The difference is in whether that change is there to make the archive usable - and of course, for archive.today, that's not the case.