You can use the average, but TurboTax does not afford that calculation.
In TurboTax, you will have to do that calculation yourself, then when the program says the interest is limited, you can enter the amount you can deduct based on your calculation ( or simply enter the proper amount on the 1098 screen)
Yes, the IRS gets a copy of the 1098, but it is not "matched" to your input. The software uses your input to determine the deduction only.
Pub 936
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