I want to confirm: you had excess HSA contributions in 2024, but you withdrew them all before the original due date of the return (April 15, 2025). This is the $3,353.
If so, then when you are asked about last year's excess contribution, just enter zero. In fact, when you withdraw the excess in a timely manner, you answer "No" when you are even asked if you had an excess contribution, because by withdrawing the excess in a timely manner, you "cured" the excess.
You aren't supposed to have a 5329 in this case, because the 5329 reports on something like 9 different penalty situations, none of which apply to you since you withdrew the excess in a timely manner.
I keep working on my test, and it insists on showing $1,081 ( $1,020 plus $61) on line 8f (Schedule 1 1040). This is, of course, correct, though I cannot imagine why your return does not show the same thing.
But, of course, I am more concerned about your tax return than your HSA Summary. OK, go back and answer "No" to the question of "Did you overfund your HSA last year?". Then let's see what happens.
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