Simple answer. The SI correctly notes the warning was dated 1991, but it fails to ask the question as of that date. It only asks the current set up, which didn't exist pre-1999. It was the same on Chinook and others. They asked the IPT, formed in 1999, "In 1993 did you ......" and they said, correctly, No. But they didn't ask anyone who would be expected to know the truth.
In 1991 that seat would have been serviced every 12 months. If the crack testing was being done then it would have been in the seat bay. The shackle bolt would never have been fitted/removed/fitted in-situ as it is done now. Even in 1999 this was the case. Sometime after that a decision was made to extend seat servicing to two, then three years. Someone devised the new proceedure of removing the shackle bolt in-situ to accomodate crack testing as it's phase was shorter than the extended seat bay servicing times.