There isn't any way to influence the IRS to not issue a penalty for late payment of tax beforehand in this situation. If you receive a penalty, you can protest it and explain what happened and the IRS may take that into consideration. It is possible in the future that you may receive a penalty for something else and the penalty you received here may influence the IRS's decision to not rescind a future penalty.
If this is the first time you received a tax penalty during the past three years, you can request a penalty relief due to 1st time abatement of tax per the information detailed in this IRS article: 1st time offense abatement of tax penalty
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