I would assume that anyone downloading the EPUB from Kobo's website would not be sideloading it onto Kobo's devices -- we can assume therefore that they would be putting it on a tablet, that does support EPUB3.
And chances are they know what they are doing anyway... (most people who don't know what they are doing just sync from the bookstore.

)
Saying that Kobo is trying to protect the buyer from doing stupid things is a ridiculous attempt at an excuse.