Your understanding of the entries on those two boxes is correct.
However, the IRS designed both the 8889 and the 5498-SA so presumably (knock on wood) they had a reason for doing it this way.
Perhaps the IRS is maintaining reports on your account that span multiple years, in which case, it would become clear what you did year-over-year.
So long as everybody is filling the forms out according to the instructions, the IRS can't ask for anything more.
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