There are plenty of games you can play with withholdings. EX: As long as you witholdings are enough to pay last years taxes or 90% of this years you are good.
Or if your bonus is in January you can have a higher witholdings from salary and the default 25% from the bonus. Just balance it by the end of the year.
But that's just simple stuff, there are also other benefits to the company.
But it's absolutely not correct that paying people with bonuses lowers their effective tax rate.