It's just a way of reducing their fees as a final sale price percentage fee is charged on some stuff. The amount of postage, regardless of how much, is not included in this.
i.e;
£50 Final sale price (free postage) X 5% = £2.50
£2 Final sale price (£48 postage) X 5% = 1p
Same total price, big difference in fees to the seller. On common, new items, I usually sort by lowest cost inc P+P which eBay allows you to do. On rare parts it's just make sure you know what they're charging before you bid.
In my opionion eBay is far too over priced and the fact you have PayPal charges on top is a joke.