HSA Excess Contributions

While working through TT I discovered I made an excess contribution of $1,463 into my HSA during 2023.  I requested a withdrawal from the custodian which was not processed until April 18th 2024 (after the normal filing deadline of 4/15/24).  However, I am a U.S. citizen living in Costa Rica with an automatic 2 month filing extension.  I requested corrected 1099-SA and 5498-SA's from the custodian, but they said that the excess contribution will be reflected on those forms for tax year 2024 and not drafting corrected 2023 forms.  TT includes the $1,463 in other income, so that looks right.  However, I am not accounting for any earnings on it.

If I'm reading IRS Pub 969 correctly, I can avoid paying the excise tax on the $1,463 if I withdrew it "by the due date, including extensions".  Will this be an issue since the 1099 and 5498 don't reconcile to my tax return?  Is this something I should just simply document in case I get audited?  How will this impact me in 2024?  Just include any earnings on the 1099-SA as income in 2024?  Thanks