ezy308, I've been involved in the last few rounds of recruitment and asked about that cover letter upload in previous applications.
I was in the same boat as yourself and thought you needed to upload but it is simply a generic piece of text that is present on all EI applications. It is not something they change application to application if you get me, it is simply part of the make up of their site, as most applications indeed would required a cover letter normally.
The screencap that is posted above with the CV specific text is the text entered by the EI staff, and a CV is what is required. A cover letter at this point would simply make too much reading to screen effectively....You will be tested then retested and then if you meet the mark you will be closely looked at.
Later on in the process when further documentation is required, you still don't submit a cover letter even though that little message is there niggling at you, but I understand where you are coming from. Best of luck in your application.