Commentary or feedback or clarifications sought by the...

Commentary or feedback or clarifications sought by the Commonwealth is not considered a "public response". The EPA and Feds have an integrated assessment approach.
The EPA can either choose to respond to the Commonwealth's questions/response directly or they can pass it to the proponent for a direct response.
I believe it is NOT a back and forth however, so in the second scenario the EPA considers the proponents response when forming their report, the EPA doesn't need to go back to the Commonwealth.

From what I understand based on the "Bilateral agreement made under section 45 of the Environment Protection and Biodiversity Conservation Act 1999 (Cth) relating to environmental assessment" between the WA State and the Commonwealth, the WA EPA will refer to the Commonwealth as part of the assessment if the proposal impacts matters of National Environmental Security or if the proposal has a large cumulative environmental impact.

I don't know for certain but my guess is the issue regarding the Carnaby's Black Cockatoo needs assessment by the federal level since it's considered a threatened species under federal law. That's possibility 1.

It could also be that the VDT approach by VRX is deemed as having a large environmental impact and that also needs assessment/consideration by the Commonwealth.