First,
Congratulations for actually reading the code including all its notes!
FEA or actual testing can be used to derive SIFs. The reason for this approximate limit is because the assumed beam element behavior starts to cease as the D/T ratio increases. It is not a linear function either, that is D/t=99.99 OK versus D/t=100.01 not OK.
What is commonly done is to use a combination of FEA and beam element analysis to analyze the system. Addressing localized loads/ stresses via FEA.
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Best Regards,
John C. Luf