That has a good practical benefit (deduplication of files that most benefit from deduplication), but it doesn't actually solve the security problems at all, it's just choosing to make the trade off one way for large files and a different way for smaller files. If you have a legitimate reason to want privacy against data confirmation attacks then you need what you need regardless of file size.

The whole thing with deduplication is a little bit overblown anyway. You don't want a hundred copies of the same big file, but is that what really happens? Nobody wants to upload the same file a hundred times, especially if the file is very large. Once there is already a copy, passing around a link to it is much easier than uploading it again. So the most common cause for it to happen is when two totally unrelated people upload the same bit-for-bit identical file, which happens, but not so often as to be prohibitive.

And in many cases file-level deduplication is difficult or impossible anyway because users make changes to the files (like editing embedded metadata or pointlessly encapsulating a single already-compressed file into a .rar archive), so the benefits you get from deduplication are not nothing, but there are situations where it is or isn't a reasonable trade off to make against privacy.