"In what world is a company that is looking to extract a fossil...

"In what world is a company that is looking to extract a fossil fuel from the ground to use to turn into urea expecting an Assessment not required decision?"

Clearly in Neurizer's world that has been their expectation. They unilaterally withdrew their first Application two years ago, when still called Leigh Creek Energy, on the grounds that they believed there were no Protected Matters relevant to their actions and therefore they did not need to go through the Approval process.
It's important also to note that the EPBC Act is so behind the times that climate change and greenhouse gas emissions are not Protected Matters.