You know, since it's a custom cover you can do whatever the hell you want with it

. It's really your decision. I hate these logos too to be honest. I don't need that on a custom cover. I always think of customs covers like special editions, like a DVD steelbook or something. So why don't you upload both versions if you still have both on your hdd?
And for the future... we all endorse creativity, that's what makes this project so great and stand apart from all the other cover sites on the net. So when you create a cover the first thing that matters is if YOU are happy with and proud of your work. If you showcase a cover and someone requests some minor changes you (or with your blessing even someone else) can always go back to the drawing board and try to comply. As corny as that sounds, just approach it with a free mind.