Numbers still don't add up for me... but, Im an idiot, and I'm not the one who is buying the Jeep....
Here are the prices, from Milous first post, of the items you listed:
Wrangler Unlimited Sport $26,620 ($25,902)
BLACK 3-PIECE HARD TOP 795 ($708)
CONNECTIVITY GROUP 560 ($498)
SIRIUS SATELLITE RADIO (Sport) 195 ($174)
Totals: $28,170 $27,282
Affiliates price: $27,085
Under the Affiliate program, the dealer is required to show you the actual factory wholesale invoice for your Jeep. It will list the maximum price you can be charged, so no worries.