well, IMO anyone buying an aftermarket head isn't going to run stock headers anyhow, so the point of having to run a different header is silly. In his case, he's already got bbk headers, so his concern is valid.
Keep in mind, the explorer gt40 heads have slight lower compression (probably not enough to make a big difference, my bro's runs like a raped ape) and the explorer gt40 heads don't have the smog bypass tubing in the heads either. Only original mustang cobra gt40's will have those.
IMO, get whatever head is in the best shape and for the best deal. If you come across some gt40p's, sell your bbks and buy some frpp headers they're great headers and will work with all ford smallblock heads.
FYI, the valve springs on the explorer gt40 and gt40p heads won't live past 5k and change, so changing those is a MUST. I used the tfs spring kit with my p heads.
As well, if you get original cobra heads, they've got the crane valve springs already, so they "should" be just fine.