I don't think there is much you can do to apply 2025 withholding against 2024 tax, it will be on your 2025 W2.
So it sounds like you only paid tax thru withholding and no estimated tax payments for 2024, but the withholding was variable and not enough to meet safe harbor?
There is probably not much you can do to reduce the penalty in this case I don't think Annualized Income method (see interview questions under Other Tax Situations / Underpayment Penalty) will provide any relief as withholding is already treated as evenly applied against the safe harbor quarterly requirement. The more typical situation where annualizing helps is an unexpected tax event late in the year (e.g. Roth conversion) accompanied by a one-time estimated tax payment.
Not a CPA/Expert just my thoughts based on what you've described.
