Obviously, it is impossible to "merge" manifests from source WARs.
However, there is no possibility to specify own, even minimal, manifest for merged WAR file.
I suggest to add this option to plugin configuration.
From the code point of view:
use Manifest as additional parameter, map two-argument call to new function
when not null, pass Manifest as second argument to the constructor of JarOutputStream
2) UberWarMojo/WarArchiveMerger/MergedWarArchive trio:
use configuration values to create correct Manifest object
send Manifest to JarUtil in MergedWarArchive.store()