Admittedly, it may seem a bit strange, but that's because the Common Affiliate Program Settings were added more recently, as we'd only had product-specific Affiliate settings before.
Once we added the Common settings, it made more sense to put the sign-up link code on that screen, since all Affiliates will join your program by clicking the same link regardless of which products you may have a program for, and since many Sellers will only use the Common settings and may never bother with product-specific settings for their Affiliate program.
You may find these links helpful for more details about how our Affiliate features and the various link types work:
http://www.e-junkie.com/ej/help.affiliates.htm
http://www.e-junkie.com/bb/topic/2690