Yes, you're right. The doctype should really be
(and the content should be valid xhtml 1.1) to avoid any problems.
I must admit I'm still a little confused about all this DTD stuff (I'm no expert). The IDPF specs spend some time talking about backwards compatibility, which suggests that it should be possible to use older specs, though any new document should be using the current one, of course.
Making sure that ePubs pass epubcheck is very sensible for publishers. They want a file that they can archive away and won't have to spend time and money to fix because it doesn't render correctly on a new ereader a few years down the road.