Think about it, there is not a single off the shelf enterprise accounting system designed to accommodate even a fraction of this maniacal minutia.
Note that the cited list didn’t account for JIEDO appropriation type (which also had a FY component) which was prevalent over the past 20 years, but is now defunct.
A major part of the problem (save the super fragmented parsing of the funding) is that each service has their own accounting & execution systems. There is NOT a singular DoD system.
https://acqnotes.com/acqnote/acquisitions/appropriation-cate...
https://ndiatvc.org/images/downloads/DAU_Training/dau_color_...
And I'm no accountant but I suspect there could be a reasonable middle ground between accounting for every single dollar spent, and accounting for 2.3 trillion dollars.
I think this is related to the very long DoD audit process, and there's a difference between being unable to track those dollars and them being missing or stolen or inappropriately used.
Notably, it took until about 2017 for annual audits to actually start at DoD, and AFAIK, they have yet to have a 'clean' audit where all/substantially all assets and spending is accounted for, although it seems like progress is being made. This isn't necessarily unexpected as the organization wasn't built with auditing as a requirement and it takes some time to retrofit that into a large organization. Congressional oversight is powerful, but persistant focus is hard to come by and is really needed on something like this.
https://www.reddit.com/r/AskHistorians/comments/pldkd4/what_...
https://www.politico.com/story/2016/06/trump-us-troop-stole-...