Hi David,
At this point in time, that ticket is unclaimed:
https://github.com/DSpace/DSpace/issues/9987 DSpace is fully built/supported by volunteers (we have no central development team to assign tickets to). So, this ticket is waiting on someone in the community to help us dig into the code to see if there's a way to support this in the "server-boot" installation approach.
So, unfortunately, at this time, we don't have an answer to your question until someone can help us to investigate if there's a solution to this problem.
In the meantime, the only approaches I can suggest are to *not use* "server-boot" (i.e. move back to installing Tomcat manually, as it sounds like you are doing), or consider moving your code directly into the "dspace-api" or "dspace-server-webapp" modules (which is less ideal, I know, because your code is no longer separated)
Once someone has claimed that ticket we should know more. If anyone is watching this thread and is interested in helping out, please feel free to claim the ticket (by simply adding comment to the ticket letting us know you are investigating it)
Tim