It is possible that several servers may share a runtime, but have different command line arguments.
The DataSourceXmlDeployer class uses the following code to decide which server to publish to:

IServer[] servers = ServerCore.getServers();
for (IServer server : servers) {
String primaryName = primaryRuntime.getName();
IRuntime runtime = server.getRuntime();
if(runtime!=null) {
String serverName = runtime.getName();
if(primaryName.equals(serverName))

}
}

This code will select the last server that matches the runtime. If several match, the last one is chosen.
Perhaps it'd be better if the Seam Project page had a section where the user could select manually which server to deploy to if several match.