There is no need for an explanatory note with regard to this. The IRS is responsible for the instructions for Form 5498-SA which specify that an HSA contribution made between January 1 and April 15 for the previous year is to be included on both years' Forms 5498-SA in the way described, so the IRS should understand what is expected under these circumstances. It's quite common for people to make such an HSA contribution and receive reporting similar to yours. As you found, the contribution reported by the HSA custodian for 2017 ($0) is the amount in box 2 of the 2017 Form 5498-SA minus the amount in box 3 of the 2016 Form 5498-SA (the total amount contributed in 2017 minus the amount contributed in 2017 that was for 2016).
