Box 9a does not have any impact on the taxable amount of your IRA distribution. If the amount in Box 1 was not the actual amount you received and instead was 100% of the Inherited IRA the percentage in this box would be used to calculate your taxable amount. Your 1099-R is correct.
You are correct, the question is just to determine whether or not a penalty should be calculated. It doesn't matter what you enter. The total amount of the distribution would be fine, as would $0 (which is the correct amount if your mother had not yet reached the age requiring RMDs).
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