PR189 Gross Up Calculation

I read an article on mylawson.com that said if we try to use PR189 for a bonus payment that any percentage based 403(b) deductions won't be taken and that we have to use PR89 instead and then enter the time records manually. I just want to make sure before we do this that there is no other way to make PR189 work. Doesn't seem to make sense since every employer that offers a pre-tax retirement plan probably offers a percentage basis plan which renders the PR189 useless. Any thoughts would be appreciated.