I am having the same issue with this and wanted a second opinion. When I finally get the "self-employed health insurance deduction" + "total premium tax credit" to equal the "monthly enrollment premiums" the repayment limitation kicks in. They have an "excess advance payment" based on the fact that their self-employed health insurance deduction puts them under the 401%.

Am I doing this correctly? It seems strange because now they get to 'keep' the "excess advance payment" even though they never really received the money. 

They way I read the instructions is that you can use any method you want but (Form 8962, line 24) + (Schedule 1, Line 16) has to be less than or equal to Form 8962, Line 11(a). 

Anyone else able to confirm this?