in theory, it's true that the new system is more accurate. in practise however, it will almost always over-deduct if you are not savvy enough about tax matters to inform your HR Dept to make the necessary deductions beforehand (such as medical ins, books, purchasing new computer, medical for parents etc). This puts additional work burden on the HR.

furthermore, there is additional duty of the HR to satisfy themselves that your request for deductions are genuine and not simply taruh one. otherwise if there is any tax evasion on your part, the IRB may punish your company as well for "abetting" it.
Thus many companies are reluctant to allow such adhoc deductions.

Under the old system, many ppl are already overpaying..thus you always hear complains about the inefficiency of IRB in refunding the money. Now with this new system, they will be more of such cases. What IRB should do is to pay interest on this monies that are overpaid until such time when they refund.