Just a guess ... But it seems that the spec is for the F-35B to carry 4 of these Bombs. There is nothing in the ref texts to indicate that the physical size of the Stores Bay (although smaller than other variants) is at fault. My guess would be that LM can't get all 4 Bombs aboard without re-routing/re-designing the hydraulic line/bracket mentioned ... But as I said ... Just a guess
As to cost ... If the original spec was for the Boeing SDB I then Raytheon who are now to provide the SDB II, need to fund the MOD's ?