Benefits : No fees -- iDevAffiliate, which does appear to be the best choice, is $200 one time (if you can install it; it won't install on my system) or $40 or more per month. Flexibility -- No limits on what you can do with the data vs. only what the affiliate tracker product or service provider offers. Secure -- Data doesn't leave your server.
Costs : You have to do it yourself or hire someone. But this should be much less than the cost of affiliate software.