I don’t think this is accurate. Java programs often require copying resource files into the JARs into special places and annotation processors to do code generation. There’s also commonly logic for renaming dependencies to deal with classpath collisions.
I agree that mismatches between packaging and build tools is frustrating. Trying to recreate all the necessary build logic for N packages is a huge effort and probably will result in a new build/packaging tool with its own inconsistencies for future folks to contend with. Definitely worth studying if the existing systems can be adapted or extended to suit your needs and getting an idea of the relative effort.