You need to use the 1.5 VM to run Eclipse and therefore the Matisse plugin, *but* that doesn’t lock you into using 1.5 to actually run Tomcat. You specify the JDK you want to run your app server with from the app server connector page.
Also, any app you develop with Matisse4MyEclipse is backward compatible as it’s all just valid Swing. I know to alteast JDK 1.4, but I’m not sure if 1.2 or 1.3 is supported.