I checked this when I specced out my Mac Pro. The Mac Pros come with 3 years warranty for HE students. This is basically the same as the standard 1 year warranty (i.e. without long term phone support) but extended to 3 years. Unlike Applecare, it does not cover a display if you purchase a display at the same time as the Mac Pro. Apple Displays only come with 1 year warranty even in the HE store. This is why I ponied up the £50 to get the full 3 years worth of Applecare on the system, which brings up the warranty on my ACD to 3 years to match up with the Mac Pro and also includes phone support for the full 3 years.
Also you don't have to use the online Apple HE Store to order, simply call 0800 039 1010, press 3 then 3 again and tell them that you are eligible to the Higher Education discount. I don't think they even asked me which University I went to, let alone my student ID or NUS number. They were very helpful with my order as well, so far things seem to be going well (although I'm knocking a piece of wood three times as I write this).