This is kinda old thread to reply, but I've been recently looking at this too.
I was using OperaFS and a tool called autohotkey that automatically does timed keystrokes to select compile, type the cd directory, and tab through the buttons to press and do the process. This was setup by someone else helping me back in time to start building something on the 3DO.
But I still wanted command line option. OperaFS doesn't have.
Then I tried your tool
OperaTool which is what I needed but I realized it does something wrong and after finally using the other 3DOEncrypt tool, it just fails to boot even on emulators.
I was about to check the source code of OperaTool and understand what's going wrong (if I am lucky, I am totally illiterate considering the Opera file system and the encryption) however I found another tool. It's not mentioned too much.
Versus posted some time ago a zip file which would compile Doom on Windows in one click
https://yadi.sk/d/jFRnqFx0iCtPS
I was like, and what about the OperaFS creation?
It seems that in that zip there is a less known tool called 3doiso.exe which takes command line and after I also run the 3DOEncrypt, it finally works (on emulator at least, but I guess that would mean real 3DO too, I will test at some point)
So, I guess there is a way for me (but not sure for people working on mac or linux, we'd need source code of these, or maybe the OperaTool could also be fixed, I wish I can find some time to understand more about it and see if I can help fix it). I agree we need more tools (but there are many I didn't know already).