The business of government is a year-long process. Given the fact that the main estimates, for instance, under the Standing Orders are required to be tabled by March 1 every year, if there's a budget after the main estimates are tabled, those initiatives in the budget will have been identified as priorities to go forward that require funding. If it's funding that's identified for the next fiscal year, then in order to be able to seek approval for that, it needs to be reflected in the supplementary estimates.
I guess the answer to your question is that if everyone knew.... If everything were static, if the main estimates existed and nothing changed in life and there were no other initiatives going on, then you might not need supplementary estimates, but that has not been the experience since 1867.