Adam...
Only one Commercial Company has ever complained about the use if its Property/Logo/Trademark in OS skinning, and that is Apple.
We have a choice. We either comply with demands/concerns of Apple or we close down totally.
You can guess the chosen course of action.
Uploading and/or displaying the Apple Logo without permission is a violation of their copyright and they are entitled to complain.
Whether you like it or not, that's just too bad.
Nothing is going to change.
Delete any logos belonging to Apple and resubmit.
Fortunately for most/all, Microsoft clearly is quite happy with incidental use of its graphics/images/logos as I expect it is seen as promoting their whares, whereas Apple sees use of theirs on a rival platform as a dilution/debasement of their product identity....