As far as I can tell, the idea of the "weapons pack" was more to allow rapid reloading of the missiles, rather like the Hunter's gun pack system did with it's guns. It allowed the swapping over of two missiles, their coolant bottles and the electronics just went with them.
As for the problem of the fin, I think they found that either they had to lengthen the nose or provide a bigger fin to ensure sufficient control of the aircraft with the larger finned Red Tops up front. They opted for the easier, initial taller fin and when that didn't work out, went for a taller, broader fin on the F.6.
So, you can either go for a longer nosed Lightning or one with a broader, taller fin. I wonder what that would have done to the drag?