So I checked, and this morning received an email from them apologising and saying that the logo can be deleted and stil be acceptable. (I notice they didn't say they'd delete it at the source!)
I subsequently replied asking EASA to change the form to take out the offending super-size logo on the /doc comment form and replace it with a more manageable one, and they've actioned it same day - so downloads and sending back replies should be reasonably fast now.