I have done some selling on ebay in the past, but I've found better online venues for my business. I don't care for their particular auction format, as I have long felt that it encourages too much sniping. I've read all the debates pro and con, but I still feel it is a form of cheating and avoiding having to make a fair bid.
It's a good idea for anyone who sells their work online to pursue multiple venues. Avoid making your business excessively dependent on any one particular venue, because any of them can decide (as ebay seems to be doing) that they don't want or need the particular kind of business you are offering. They do have the right to make those kinds of choices. Fortunately, as you have pointed out, for any that decide they don't want your business, there are others who do.
That being said, I just took a look at their shipping policy, and don't see anything that prohibits sellers from charging a fair shipping fee that covers all the real costs, so I'm not sure what you're referring to.
Kate