The difference is more if you spend more. It also used to vary in the FE/HE store depending on how much your school spent annually with Apple - have loads of Macs on campus and your personal one would be discounted more. not sure if that is still that case, but if it is the the numbers I pulled off my Uni site may vary slightly.
iMac 21.5" entry level is £60 cheaper through my HE Apple store
iMac 27" i5 is £100 cheaper
Mac Mini is £20 cheaper
The biggest difference is that buying through the normal Education store gives you the standard 1 year warranty whereas the National Higher Education agreement has an added clause:
10.1.1 All Apple-branded desktop and portable computer products shall be subject to a 36 calendar month warranty period commencing from the date of delivery.
That 3 years is a big difference. To get that iMac i5 through the normal store with the 3 years requires an additional £115 for the Applecare - making the difference over £200.
I have had the logic board on my laptop replaced (in year 2) and two HDD bays on my desktop rewired (in year 3), which initially I had been told was a logic board problem as well.
If you can wait until school starts I would...