Ok, so I actually did this sooner than I thought I would
If anyone else is having the same problem as me, here is the full solution I made. This will create a file called RES-INDEX in the resources directory which stores paths to all other resources. It uses this file when trying to discover resources to load. Now I can use my code in jar as well as in IntelliJ.
Then you make your code call ResourceIndexer on the pre-package step of Maven Package: