It's certainly true that the summary-level financial statements of the Government of Canada don't typically get into a level of detail that might pick up an individual program. It is a consolidated statement. There is some segmented information that gives expenditures in total by departments and that sort of thing, but indeed there's a limited amount of fine detail in the audited financial statements.
Of course, the other volumes of the public accounts, and the other sections of volume I in which the summary report is embedded, do contain more detail. There are also other accountability documents prepared, departmental performance reports and that sort of thing, and quarterly financial statements.
The public accounts serve a particular purpose. It's not the only accountability document, and you would need to look at other sources for certain questions.