Yes, I think context plays an important part. I suppose you might ask yourself why the owners of the character or the original artist are not being asked to provide artwork if that particular character is needed for the cover. Do they charge too much or are they too busy (the latter usually effects the former)? In which case they might not be pleased if an artist is found who will possibly copy for less money (or for free!).
This might not be the case for you, of course. As mentioned, if you are highlighting a product, a review or whatever, then it might be different and the best course of action would be to talk to the magazine editor and make sure it's their decision and that they seek the necessary permission. If there is any trouble, you want to make sure that someone else will foot the bill if it comes to the worst.
"Gallery" work might be different and if you are the one being highlighted then it seems to me that you should be ok, especially of you are not making any money from it. It would be the magazine's responsibility. But if fan art on the cover creates a problem for the magazine then you are not doing yourself any favours by submitting it for "potential use on the cover".