Hold on. I'm missing what the issue is here this sounds like fairly typical stuff? I must admit to not having ploughed through several pages of various posters arguing though, so I should sort that out I guess.
From a snapshot view though any development like this has staged drops of various bits of capability/function. Ultimately it'll be the customer that agrees and signs off those drops. Any variances or non qualifications would also have to signed off. It's only an issue when it never happens or an alternative solution is not acheivable. BIT/CBIT and IBIT is one of those things that always seems to happen near the end anyway.
As for the whole 'oh noes my engine has gone' there's FOD up it, its really dangerous' I don't see how any naval jet aircraft is exempt from this sort of problem. Is this not a basic issue with trying to get an aircraft on a tiny strip of metal in the sea? Though on an aircraft carrier/LHA/LHD would'nt there be FOD checks etc. Or have I missed some additional bit of hysteria somewhere?