Yes, for the created Form 1099-R you will enter the over contribution in boxes 1 and 2a. In box 7 you will use code P. For the earnings, you will get next year a Form 1099-R with code 8 that will be included on your 2023 tax return.
Yes, the warning won't go away because it is only triggered by the amount in box 12 from the W-2. But for excess deferrals, there won't be any penalties calculated so you can ignore the message for now. You got the excess and earnings distributed and reported it correctly.
@SJH57
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