Yes, that's correct. However, since Form 5329 is considered to be a stand-alone tax return, you can probably just file 2017 and 2018 Forms 5329 and omit Form 1040X. However, there is generally nothing wrong with including Form 1040X to show that there is no other change to your tax return.
After the due date of your 2016 tax return, the only way to resolve the excess is to make a regular taxable (not applied to medical expenses) distribution from the HSA. If you made any distributions from the HSA in 2017 or 2018 that on Form 8889 you originally reported as used for medical expenses, you can amend one or both years to change Form 8889 to indicate that the distribution was not used for medical expenses, therefore making it taxable and going toward reducing the excess. Presumably you were age 65 or over in 2016, so you would not incur and early-distribution penalty on these as taxable distributions. If you make this change your amendment would need to include Forms 1040X, 8889 and 5329. (If you can resolve the entire excess in this way with the amendment to your 2017 tax return, you won't need to amend 2018.) If you did not make any distributions from the HSA in 2017 or 2018, you'll need to make a taxable distribution from the HSA before the end of 2019 to avoid another 6% penalty for 2019.
