The feeling on the mailing list was that the M4 release should offer separate Tomcat and Jetty builds. If that is to be done, I think we essentially want two versions of the J2EE server plan that are otherwise identical, or one with two different possible imports for the web container, or whatever. With the current plans it appears that your options are Jetty or Jetty+Tomcat, not Tomcat alone (at least, not without manual editing). After installation, I think we want the org/apache/geronimo/Server configuration to have either Tomcat or Jetty but not both (and no separate org/apache/geronimo/Tomcat configuration).
Note that it should be quite easy to build two separate installer packages based on this, and it may be possible to build one installer that includes one app server by default but allows you to override it with the other. I'm not sure it will be as easy to have two separate assembly output directories; perhaps the server selected for the assembly module should be controlled by a property in assembly/project.properties
It would probably be best for this ultimately to migrate to HEAD, but it's urgent that we have it in the M4 branch (based on the apparent concensus)