withBundledScalaContainers doesn't define a container

I have EclipseKeys.withBundledScalaContainers := false in my build.sbt. But this line disappears:

  <classpathentry kind="con" path="org.scala-ide.sdt.launching.SCALA_CONTAINER"/>

And I get only:

  <classpathentry sourcepath="/home/muhuk/.ivy2/cache/org.scala-lang/scala-library/srcs/scala-library-2.12.1-sources.jar" kind="lib" path="/home/muhuk/.ivy2/cache/org.scala-lang/scala-library/jars/scala-library-2.12.1.jar">
  <classpathentry sourcepath="/home/muhuk/.ivy2/cache/org.scala-lang/scala-reflect/srcs/scala-reflect-2.12.1-sources.jar" kind="lib" path="/home/muhuk/.ivy2/cache/org.sca

la-lang/scala-reflect/jars/scala-reflect-2.12.1.jar">

And no scala compiler.

When I reopen the project in eclipse, there is no container. And I get the following error:

The version of scala library found in the build path (2.12.1) is incompatible with the one 
expected by scala IDE (2.11.8). Please replace the scala library with the scala container 
or a compatible scala library jar.

I tried to follow BYOS instructions but the library and the compiler sits in different directories (in ivy cache) and it seems to expect them in one place. Besides my understanding is with withBundledScalaContainers you don't need BYOS.

Am I missing something?

sbt 0.13.13 (scala 2.10.6)
Eclipse 4.6.2
Scala IDE 4.5.0

Reproduce the generated Eclipse project with EclipseKeys.withBundledScalaContainers := false using the reported sbt 0.13.13, Eclipse 4.6.2, and Scala IDE 4.5.0 versions. Compare the resulting .classpath with the expected Scala container, library, and compiler entries; done means reopening the project no longer reports the incompatible Scala library configuration.