In a word.
There was no spiritual energy in the Federation.
The spiritual energy revival was wrong. The reason why spiritual energy appeared in the Federation's world was that the Federation's Quantum Experiment Center opened a quantum space channel that led to the Great Desolate World 50 years ago.
The passageway between the two worlds opened, attracting the spiritual energy of the Great Desolate World to the Federation.
It was like two water bottles.
The world of the Federation was an empty water bottle, and the world of the Great Desolate World was a water bottle filled with water.
Originally, there was no connection between the two worlds. They lived side by side without any interference. However, the passageway that was opened connected the two water bottles together.