That's again a clear question that calls for hopefully a clear answer, but it might be difficult to answer briefly on this one.
I think there are many steps that could be taken to achieve the stated objective of making these documents more readable. I think one obvious first step, which I mention often, is to better align the estimates process with the budget process. Then when the main estimates are tabled, we would be able find budget items more easily. If the main estimates are tabled before the budget, they don't include what is in the budget, so aligning the two would be a very good first step.
The other aspect I would recommend is something I try to do myself, but it is very difficult: writing in plain language. It's especially difficult when the text is drafted by bureaucrats in various departments. They all want to be as precise as possible, but they don't have a common culture of writing in plain language. I'm guilty, and my office is guilty, of not doing that.
Having a budget that is tabled at a fixed date or within a short window would certainly allow for better alignment between the main estimates and the supplementary estimates. That would make it easier for people like you and your colleagues to hold the government to account and to scrutinize these very important pieces of of legislation and these accountability documents.