why unaligned apk is needed?
It is a two step process. The unaligned apk is just an intermediate product.
- the unaligned apk is generated
- the unaligned gets aligned and produces the aligned apk
The unaligned(signed) APK is needed because signing an aligned apk will undo the alignment.
From the docs:
Caution: zipalign must only be performed after the .apk file has been signed with your private key. If you perform zipalign before signing, then the signing procedure will undo the alignment.
See this answer for more. Here is the detailed build process: