Step to reproduce
1) create a project with multiple pmml files, each in its own package (eg. resources/package_name/file.pmml)
2) create a kmodule xml and define one kiebase for each package
3) compile the kjar
4) in the kjar the files/classes are all in the proper place (i.e. in the expected package)
5) add the kjar in a new project
6) in the new project invoke
KieServices.get().newKieClasspathContainer().getKieBase(kbaseName);
The jar packages are inside the kieBase.getPackages(), but they are not marked as "PMMLType" packages - so it is necessary to invoke the (PMML)AssemblerService to wrap the content of the (jar) packages inside correct PMMLType packages and put them in the knowledge base

The following snippet is a temporary workaround (inside CanonicalKieModule.createKieBase(KieBaseModelImpl, KieProject, ResultsImpl, KieBaseConfiguration))

for (KiePackage pk : pkgs) {
                // Workaround to "mark" already compiled packages (as found inside the kjar and retrieved by createKiePackages(kieProject, kBaseModel, messages, kBaseConf))
                // as "PMML" packages
                boolean isInternalKnowldgePackage = pk instanceof InternalKnowledgePackage;
                final InternalKnowledgePackage originalPackage = kieBase.getPackage(pk.getName());
                if (originalPackage != null && isInternalKnowldgePackage && ((InternalKnowledgePackage) pk).getResourceTypePackages().get(ResourceType.PMML) != null) {
                    originalPackage.getResourceTypePackages().put(ResourceType.PMML, ((InternalKnowledgePackage) pk).getResourceTypePackages().get(ResourceType.PMML));
                } else if (originalPackage == null) {
                    kieBase.addPackages(pkgs);
                }
            }

The idea is to get the "type" information from newly compiled package and put it in the existing one (that also contains al the other compiled classes).
Ideally, we should be able to completely skip the (PMML)AssemblerService invocation (that recreate new packages)