The supplementary estimates (A) are relatively new introductions to the cycle. It was done at the request of parliamentarians and the Auditor General, who called for more timely allocation of appropriated money to departments.
In the previous construct, when the first supplementary estimates of the year were in the fall, Parliament wasn't approving that appropriation until December, so nine-twelfths of the fiscal year had elapsed before departments were getting their money. With supplementary (A)s, that money's being voted to departments three months into the fiscal year. As Bill mentions, a significant portion of this is related to budget initiatives or other priorities of the government.
It adds to complexity by introducing another piece in the cycle, but it's motivated by timeliness.