Hi Shyam,
yes, there is this difference in IE and Chrome, ZIP and SCA files. But this is happening in Netweaver 7.0X. This doesn't happening in 7.4 packages as example.
Regarding the application-j2ee-engine.xml, this is not a mandatory file for all packages. For example, I donwloaded the CORETOOLS14P_9-1006497.zip and also SCA and none of them have this file. But the SAP_MANIFEST.MF with many component information are there in both.
Thanks,
Marcelo Pinheiro