Agree with that there are two options, but you do pay 6% penalty with option 1 ("apply the overage to the next year's qualifying amount"). Unofficial but correct reference: https://www.wageworks.com/employees/support-center/support-and-faq/healthcare/hsa/what-happens-if-i-...

To add the excess employer contribution to income, you put "1" on "report excess employer contributions as other income" field on HSA input screen.