I did review this and do a lot of testing a couple versions back. I had also questioned Microsoft about it. However, there is a document called T4127 Payroll deductions formulas for Computer Programs, which Microsoft was advised to use. So the calculations will be different depending on when the employee started and how much is added using a lump sum.
However, I have found that if the employee starts January 1 and has a normal payroll the calculations on-line are almost identical (within a few cents). If you run a test batch for the first pay period of the year on a new test employee and this is not the result then you should check your Employee TD1 values and your paycode tax rules.
I do agree that this disconnect with other types of payroll can be a problem, but it is what CRA told Microsoft they had to do.
Every year CRA provides a list of specific changes that are required. Microsoft does not guess at these changes or decided there is a better way. They do as they are told. So really if we can get CRA to listen that is where the change will come from.
Debra