I asked a question similar to yours a while back. Buildship does execute eclipse and eclipseWtp tasks if such tasks are available (from applying the plugins). It does this on gradle 3.0+.
It does not do this for earlier versions of gradle because those tasks were essentially busted.
You could make one of those tasks depend on your custom task, or make your custom task run after one of those via mustRunAfter
Also note that buildship is a young project still very much in development. You could offer your suggestions as issues in github as well.