You are misreading it.  Go back and re-read it and actually fill out the numbers  in the worksheet.  Line 14 does the percentage.

https://www.irs.gov/pub/irs-pdf/p936.pdf#page=12

Again, think of it logically.  If there were two separate loans, the loan for Acquisition Debt would be deductible.  That isn't going to change just because two loans are combined into one loan.