As you said, when the main estimates are presented prior to the federal budget, new measures introduced in the federal budget are not reflected in the main estimates and must be included in the supplementary estimates. Statutory programs, on the other hand, are directly funded through enabling legislation.
When measures are not in the main estimates but rather in supplementary estimates, this effectively lengthens the timeframe, because it takes time for funding to be requested from Treasury Board, for funding to be provided, for programs to be put in place, and for the government to finally spend the money.
That said, when there are emergencies such as COVID-19, the government can significantly shorten these timelines by expediting internal procedures. The extent of the negative impact on the disbursement of funds, assistance to the population and equipment purchases therefore depends on the ability and willingness of the government to shorten the timeframe through these internal approvals.