Smiddy and freddo are correct. To expand on that:
The ARC is not a Court. Its powers are limited. It is essentially an inquisitorial body, that has incredible powers to subpoena people and documents, and then cross-examine. With the information gathered, it writes a report. And that is it.
Sometimes, a Royal Commission will also refer matters to the appropriate State or Federal Public Prosecutor, but because of the nature of this RC, it is not likely.
Justice Peter McClellan is a judge of the NSW Court of Appeal, but his appointment as Royal Commissioner is a completely separate role. The Australian Federal Court has no role (apart from a technical role that I won't confuse you with). Jurisdiction in any likely civil or criminal case rests with the relevant State or Territory, and will be run independently of the RC.
There will be no negotiated settlement. It just does not work like that. This is not a USA-style investigation. Possibly, if Watchtower is able to demonstrate that it has changed its internal procedures, it might be mentioned in the final report.
I haven't been following developments closely, but my guess is that we wont know whether the submissions of Counsel assisting the Commissioner in relation to Watchtower were accepted, for a while yet. (The RC has been dealing with a number of other organisations, particularly the Catholic Church.) If the submissions are accepted, the effects as I see it, would be as follows:
What more do I need to say! Further, any journalist will just report the outcome and findings. They treat it like a Court decision.
2. Civil proceedings
This is the biggest impact. If any victim wants to sue Watchtower (not just the the individual perpetrator) for civil damages in an Australian Court, then the task will be way way easier. No need to subpoena the relevant secret Elders Book or cross-examine an Elder on how a JC is run. The victim's lawyer could just submit the ARC report as evidence of Watchtower's flawed internal processes. 80% of the task is done for them, which of course dramatically reduces the costs and risks of running a case on behalf of a victim.
3. Criminal proceedings
It may possibly assist some criminal proceedings, but this is a complicated topic.