PackageParserException: Package ...base.apk has no certificates at entry AndroidManifest.xml
Today I've updated Android Studio to 3.3 and encountered the same issue.
I fixed it after delete Build folder, Clean Project, Invalidate Caches/Restart. And after that I could generate signed application via Build -> Generate Signed Bundle/APK with only V1 signature.
Build signed application with signingConfigs release still doesn't work.
You can try my solution.