I totally understand what you are asking and have run into the same issue many times.
Retirement plans usually require the deduction and matching from all wages including bonuses. I don't understand why this is not included on the bonus only calculations at least as an option. If anyone finds the settings to make this change please reply!
The only work-around that I have found is to create another regular paycheck and do a lot of manipulating to remove the deductions and accruals that shouldn't come out of a bonus check. Keep in mind that also sends a workforce notification to the employee of another pay stub which is not great for a surprise bonus.
