I might not be using this tool correctly, because it does not work.
In what way?
Being able to tell Hatari on the command line to enter the debugger on an ILLEGAL instruction is what I had hoped for.
I think you have misunderstood what the tool does. It's a helper script which tells you what you need to write to the debugger. So in your case you are interested in the ILLEGAL instruction and the tool tells you that its opcode is $4afc, so the right command to write after entering the debugger is "b (pc).w = $4afc" (and continue).
To me this looks like exactly what you asked for.