I guess I'll stop saying how surprised I am at a lot of this stuff, but I just played my recently acquired Boredoms disc, 'Sea Drum/House of Sun'. The first track only was HDCD, the second was not. It only has two tracks, each over 20 minutes long. I have the NA domestic version, I have no idea if the original Japanese version from last year would be the same or not, maybe someone else has it.
Still haven't gotten that Jack Johnson disc yet, but it won't be long.