Form 1099-SA reports on distributions from your HSA. Form 5498-SA reports on contributions to your HSA and the fair market value of the HSA.
So the two forms aren't reporting the same thing, and what is true for one is not true for the other.
On the 1099-SA, box 2 (if filled) certainly should be smaller than box 1, because box two is the earnings on an excess contribution whole box 1 (if filled) is the excess contribution.
Unless you have rates of return well in excess of 100%, the earnings will always be smaller than the excess itself.
In the case of the 5498-SA, box 1 is MSA contributions (if any) and box 2 is total contributions.
But you don't enter form 5498-SA into TurboTax anyway, so this won't matter.
