I cannot confirm the problem. I have set up a game with the EA, one empire under human control, the other computer with high bonus.
In the next step I activated the ministers for the human empire except for ship movement (so no colonies were set up) and de-activated ministers in the computer empire likewise.
After some turns the human empire hit the maintenance limit with 8 ships, using up some of the stored resources.
The computer empire had build 15 ships in this time. It had crossed the maintenance limit by 5k minerals (because the bonus was now gone after human control). It still had full storages, a sign that it had no lack of minerals at all in the past turns.
My conclusion is that bonus are working quite well.
