When producing an APP, a DMG or a PKG the name of the bundle can be set by the user according INSTALLER_NAME.
In the case of a PKG for the Mac App Store the packager adds "-MacAppStore":

./java/com/oracle/tools/packager/mac/MacAppStoreBundler.java: File finalPKG = new File(outdir, INSTALLER_NAME.fetchFrom(p)+"-MacAppStore.pkg");

A tool written on top of the packager API must take into account such a hidden rule, which is asking for confusion and creates an adherence to an implementation detail.
Unless I missed something I suggest to do in Mac App Store cases as for every others.