Yes, the excess deferral is added to you taxable income on line 1h of Form 1040 and will be taxed according to your tax bracket. You shouldn't see any penalty when you follow the steps above.
To clarify, you made a Roth IRA contribution with the funds received from the excess deferral? If the contribution was made for 2024 then you will enter it in the IRA contribution interview under Deductions & Credits.
You also converted funds from a Traditional IRA to Roth IRA? If this happened in 2025 then you will get a 2025 Form 1099-R and report this next year on your 2025 return. If your spouse made nonductile contributions to the Traditional IRA for 2024 then please see How do I enter a backdoor Roth IRA conversion? for additional information.
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