As Opus 17 mentioned, Vanguard's instruction appears to describes the procedure for obtaining a return of contribution before the (extended) due date of your 2023 tax return. Since it's now past October 15, 2024, the deadline for doing than, I'm not sure that you can treat the $4,600 as an excess contribution unless some or all of it would be an excess contribution when treated as a regular personal traditional IRA contribution.
Since it's now 2025, treating the $4,600 as an excess traditional IRA contribution would subject to to a 6%, $276 penalty on your amended 2023 tax return and again on your 2024 tax return. If the $4,600 would not be an excess contribution for 2023, I think that the best approach would be to report it as a regular personal traditional IRA contribution on your amended 2023 tax return and be done with it. (If your 2023 MAGI for the purpose would make it a nondeductible contribution, you'll need to track that on Form 8606 going forward.)
Oh, and given how late the replacement code-G Form 1099-R came, it has to be a CORRECTED form since Vanguard would have sent the original to the IRA long ago. Vanguard should have marked the CORRECTED box on the form.
