When I eclipse generate my projects none of the plugins in project/plugins.sbt have corresponding <classpathentry sourcepath="..."> entries in the project's generated .classpath file. For library dependencies, no problem, sourcepath entries are generated correctly.
Running coursier the target plugins and their sources are downloaded so the sources are available on the file system.
// example /project/plugins.sbt
"com.typesafe.play" % "sbt-plugin" % "2.6.0-M4" withSources
sbt 0.13.15
scala 2.12.2
sbteclipse 5.1.0