Yes, it will be apparent that a 2024 8606 that is signed by you and mailed to the IRS is a form that you'd like added to your record.
If you'd prefer, you certainly can add a letter. You could include a brief cover letter with your mailing to help the IRS process your form. Your letter should clearly state your full name, current address, and Social Security number at the top. Explain that you are sending a standalone Form 8606 for the 2024 tax year to report IRA contributions that were left off your original return.
Since you are writing the letter, you could also request they waive the $50 late penalty. To avoid the penalty, you should explain in your own words that you didn’t realize a separate form was necessary because your tax total stayed the same, but you are proactively fixing the error now to ensure your future retirement records are correct. It is important to specifically use the phrase "reasonable cause" in your explanation to let the IRS know you made an honest mistake in good faith and are requesting they waive the $50 fee.
