Both the 12 and 13 SE trim has auto-lamps. The 13's also have a trunk release button on the headlight switch. Not sure on the price difference - seems like the switch was in the $40 range on Ford Parts also - but I might have been looking at the 13 version there.
On the BCM - I knew a brand new unit would need to be re-flashed, but I thought the dealer usually did that for the price of the unit (similar to if you replace a speedo cluster - they will usually program your existing mileage into it for free, but if you bring in a used one they charge a lot to re-program it).
I didn't realize enabling the fog lights in IDS was different from flashing the BCM - if so, that is good news also.
Do you have access to the Service Manual? - I'm curious about upper grille replacement as well - there a word description on here, but nothing with pictures.