You're right that a pro-ration of $500 per quarter isn't correct; it lacks precision and, as you note, the IRS' instructions for the line are not helpful.
The best way to correctly allocate estimated payments each quarter is probably to closely track the performance of all of your Form 8960-relevant investment income, checking quarterly statements. This would surely be time-consuming, and your time may well be more valuable than any penalty that might be assessed.
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