I undersatand from an Authority close to a Cmdr (E) up at the Clyde ,that the Modules once built at Portsmouth,then transported up to Scotland,sometimes dont marry up to their counterparts.Even watertight doors are not able to actuate in their slots,and then small items like a Plinth onto which a Phalanx mounting is bolted,has its bolt holes not lining up with its flange plate,so someone could not even drill out from a template accurately.
Given that when last I looked, all the Portsmouth modules (with the exception of one Island) were hangar deck and below, I suspect your contact may be mistaken. The sponson modules where the CIWS live were erected at Rosyth, mainly from steel fabricated in Appledore and shipped up.
Issues with marrying up large blocks will always arise. The difference in doing them between different shipyards is that it gets contractual rather than just the heads of the steel fab and shipbuilding departments in one shipyard having a shouting match and then just fixing the problem. Mountains and molehills one suspects - possibly compounded by RN personnel with limited experiences of working in build yards (as opposed to refit).