How's it namespace pollution? It won't cause any clashes in either std or the user's code. It's just a few directories moving slightly higher up in a directory structure (which as an aside, is even deeper than you might think, because it also includes the deno.land domain, remember).
Just un-necessary pollutes the drop-down list in auto-completes when someone is coding stuff that has nothing to do with encodings. There is a reason for categorization and this change breaks it.