It is not the fact that there were dimensional differences that was a problem. That is a minor technical and programme risk common to many aircraft that, as long as you recognise it, can be dealt with easily. The initial problem is recognising it. MoD and BAeS got over that on Day 1.
The real problem (in this case) was no-one listened to the experts, primarily RAF and civvy engineers in MoD(PE) whose wailing and nashing of teeth could be heard throughout St Giles Court.
Importantly, you have to take a broader view. What else was happening in that particular area of MoD(PE) at the time? Under the same 2 Star the other cock-up of the century, Chinook HC Mk3, was taking root. Same problem. Experienced (i.e. junior) RAF and civvy staffs saying "This is madness" and being ignored.
This is not a coincidence.
MoD claim these events to be isolated and unrelated. There should be a joint inquiry. Same people involved after all. Then we'll see if they are unrelated.