By happy coincidence I received Naked Tourist's Mad Different Methods in the post a few days ago. I can understand why they chose to stick the extra track at the end, it's good but has a very different style to the rest of the album, and I imagine it would really damage the flow of the album otherwise.
BTW, I wouldn't really call tracks which play after n minutes silence "hidden" - the real way to hide a track is to stick it in the space before the first track of the album begins, like the hidden track on Ae's EP7. It was a nice surprise discovering that after I'd already had the CD for a couple of years (though actually getting at it wasn't easy, I had to use EAC in the end).