You are still administering PEOPLE.
People do things like embezzle the budget in the middle of a genocidal war. Like plan to attack and conquer a nation orders of magnitude their size.
Like argue about national secrets while facing down double digit dreadnoughts.
We've done pretty well with corruption cleaning. It mostly takes political will to out the people doing it. And not being one of them, of course. Most of the problems you list will still happen in a free market economy, just done by corporations, contractors and private agents. People we have less control and oversight over.
War isn't the place where planned economy struggles the most. Peace is, because it has less drive for change, evolution and improvement.
I don't know what your point about the reapers is. Each reaper is a nation, as they say, and they directly control everything. But they don't have the human failure aspect, so it's irrelevant.
I made a plan because I was curious:
[ ] Plan War communism
-[ ][DIPLOMACY] Hard Times, Hard Decisions
--[ ][DOUBLE DOWN]
-[ ][DIPLOMACY] Special Addresses
-[ ][ECONOMY] Nationalize Everything
-[ ][ECONOMY] Public Works Projects
-[ ][INTRIGUE] Formalize Ministerial Security
-[ ][INTRIGUE] Looking for Sponsors
-[ ][LEARNING] Crash courses
-[ ][PERSONAL] Personal Attention - Hard Times, Hard Decisions
-[ ][PERSONAL] Personal Attention - Nationalize Everything
-[ ][PERSONAL] Personal Attention - Public Works Projects
It sounds risky, and we would have to invest in reorganizing everything for a few turns, while at war. But at least we would be able to insure everyone has their basic needs met and our industrial machine keep running. We could try a write in to tone it done a little and only nationalize the most crucial industries if we don't want to face too much bureaucratic work.
Also, it's worth noting nationalizing everything doesn't mean we have to manage everything top down once the crisis passes. We could easily delegate it to more local management systems while still keeping oversight and helping the various pieces coordinate.