I'm not familiar with the SwiftPM plugin architecture, but adding some debugging Java2SwiftPlugin suggests the underlying issue is sourceModule.pluginGeneratedResources being an empty array. As such it is not finding the class files compiled by JavaCompilerPlugin, which are the ones that are subject to --swift-native-implementation.
So its sounds like there's something about my Package.swift which is messing up the plugin pipeline.
Alright: here is the fix. :) Package.swift needs to be swift-tools-version:6.0 (necessitating .swiftLanguageMode(.v5)). Footgun alert! I'll file an issue.