As long as we do not have a PDE builder plugin with Gradle, we have to add Jar-dependencies to Gradle scripts (whereas in Manifest.mf you have package definitions). So there will be a gap between Eclipse PDE build and Gradle build. You can accept this and just say: ok, development is done within Eclipse; developpers define Manifest definitions and put plugin dependencies as project or jar dependencies into Gradle scripts.
Or, you build some intelligent tool which takes your Manifest files, analyze their dependency declarations and convert them to the Gradle view of dependencies.
There is no other way around: you cannot generate Eclipse Manifest definitions from the Gradle view because Gradle has the traditional Java classpath view, not the OSGI/Eclipse view of dependencies.