Move AllowMissingDependencies handling into processMainCert

I046d75dbbd4f21f4a2b6851f558e430e9879fcff fixed android_app modules
with missing certificate dependencies when AllowMissingDependencies
was set, but the same problem can occur in android_app_import and
android_rro modules.  Move the AllowMissingDependencies handling
into processMainCert so that it applies to all of them.

Bug: 246649647
Test: TestAppImportMissingCertificateAllowMissingDependencies
Change-Id: Ic7dd3e61e0e3af15c53b583cf680b1e52394a018