If you set a flat cost for shipping, that has nothing to do with what you pay as a seller. That cost is what your buyer pays you to cover the shipping charges. You can set that whatever you want it to be. Many sellers who use flat rate shipping, like myself, have multiple Shipping Business policies set it up at different price points.
If you buy your shipping label through eBay, regardless of what type of shipping you have (flat, calculated, or "free"), you, the seller, get a discount on the cost of the label. If you use calculated shipping, you can set your account up to pass along that discount or a part of it (I think) to your buyers. If you are setting a flat rate, then you just set it up however you want to do it. If you want to charge them only for the cost of the actual label, that's fine. I would encourage you to charge a little above that to cover your fees and supplies. My flat rate policies are based on Zone 8 pricing, rounded up to the nearest .95 cents. There is always a little extra left after I buy my label. It could be as much as a few dollars if the buyer is closer to me. I do not refund differences. A normal business does not do that, so why would I? When I price items, I look at where market is at in terms of total price (item cost + shipping), and that gives me an idea of where I want to be on the out-the-door cost.
