Accepting the penalty for 2016 will not allow you to contribute more for 2017. You also have to report the HSA contribution as 2016 income. To avoid another 6% on this same $3,000 for 2017, the $3,000 excess from 2016 will have to be applied as a contribution for 2017, reducing the additional amount that your employer can contribute for 2017 to $400. Accepting the penalty will therefore do nothing but needlessly throw away $180 for the penalty.
If you fail to remain HSA-contribution eligible through at least 11 months of 2017, things get even worse since you won't even be able to apply the full $3,000 excess as a 2017 contribution. Under these circumstances, to avoid any excess contribution for 2017 you would need to take a taxable distribution from the HSA of the amount of the remaining excess. This would be the second time this money is taxed. If you are under age 65 at the time of this distribution, the distribution is also subject to a 20% early-distribution penalty. In other words, accepting the penalty for 2016 can potentially lead to much greater penalties down the road.
