I have this same issue in Pro Series and had a client's 2023 EIC (that was calculated in Pro Series) reversed by the IRS because the total W2 income flowed to line 1.

The medical waiver is subtracted on Schedule 1, line 8s which then flows to the 1040 line 8 as a negative number which eventually adjusts the AGI, but the EIC calculation the IRS used was the total income from the W2s as earned income.

The instructions for the 1040 and the Schedule 1 do not correctly address the problem.

This is the first time having this issue after many years and I just learned about it when they provided paperwork for preparing their 2024 return which included the IRS letter and is now too late to appeal.