I'm not sure I'm equipped to answer the question. It may well be institutional momentum: this is the way the reports have always been done, so this is the way they should be done today. Maybe it's going to require a shakeup from this committee, with the input of experts, saying that this is the format you want these reports to come in and that you want them provided in that format.
There are vast computer systems that track all kinds of expenditures, down to the penny level, for these departments. The question is, what do you want these computer systems to output to be useful for parliamentarians?
I don't know the history of why the estimates are the way they are, but you're certainly right in pointing out that you get much more information in most levels of government and in private industry, even publicly, than parliamentarians or Canadians appear to be getting about the federal government.