I am not sure if we can create a bundle file manually by combining two zips. However we can import multiple archive through prpcUtils.sh script.
When importing from a file system, the relative path to the archive from the \utils\ folder or the full path to the archive. If the path is a folder, the tool processes all archive files in that folder.
Any product created from "Designer Studio > Application > Distribution > Package" or "Designer Studio > Application > Distribution > Export" will generate a zip file and that zip file will contain Application.xml file and MANIFEST.MF in META-INF folder along with other jar files for schema and rules.
But it is not possible to include products like P1_04_01_02 and P2_04_01_04 in another product definition. So in this case a single product needs to defined that will contain ruleset versions 01-01-01 to 01-01-04.