We had it happen when we pulled out of a PEO. They required us to cut a final paycheck through 12/31 which would not normally have been paid until after the first of the next year. I did get lots of questions that year on W-2s since everyone was high by a paycheck. And then the next year I got lots of questions because everyone was low a paycheck. In your situation, you would not be low a paycheck so you should not get questions the second year.
You might also need to look at annual deductions for anyone who gets close to govt limits (such as 401k max deductions). If they take the max and divide by 26 pay periods rather than 27, the employee deduction will not occur in the last paycheck and possibly not get matched.
As to the budget, luckily I have a great CFO and CEO. I just let them know in advance which months will have three payrolls and they budget for it. They usually only see the extra payroll twice, but they deal with the third the same as they would for the other two.
Has anyone ever argued and implemented that the exempt salaried should have the annual rate divided by 27 that year? Since hourlies would get paid for hours worked, it would not affect them. It would be an interesting case study!