I think the main difference is that one is designed to outlast the manufacturer's warranty period (4 year 50K miles I think?) while the other is designed to last for the typical aftermarket warranty period, which is generally much less. It's simple business sense, aftermarket manufacturers have to sell for way less than OEM or nobody would buy them, so naturally they have to cut corners during manufacturing and can't offer the longer warranties.
Not that dealerships don't mark their parts way up anyway, I'm just saying that the system is perfectly designed to achieve the results you're seeing.