Hi Martin
As far as I know I've never had to implement any code involving SysOperation? I understand the default reports interface with it, but I don't need to interfere with any of their workings beyond the content of them.
The reason our company has been using RunBaseBatch was a few business requirements for running multiple reports in a loop. For these requirements, (currently) RunBaseBatch seems to handle the job fine. Again, this may change for us in the future if we ever upgrade and the class is removed, but I'm sure the same is the case for many of the built-in classes.
At any rate, I realised while waiting on a CIL build - I was overthinking the problem. I no longer have the requirement to pass the journal ID from batch :) I'll mark this as answered.