It's a possibility, especially if the Department of Finance and the Treasury Board Secretariat don't work together or don't work well together.
In my experience, having worked on several budgets, it is possible to overcome these obstacles by having the Department of Finance and the Treasury Board Secretariat work very closely together on potential and decided budget measures and having the Treasury Board Secretariat do its due diligence, possibly before the budget, so that items in the budget can also be included in the main estimates or in the supplementary estimates.