When you create an user and specify a non-local home dir, you can use the "Create home directory now" button in WGM. In this case the template used is the one on your server in /System/Library/User Template/ dir. Modify it here will modifiy all the home dir created after by using this button. In this case, you plan to use a remote home dir - the user logged on a mac "macintosh" won't leave any home dir on this macintosh - instead it is on an afp server.
If you plan to use /Users/ (meaning : [local boot disk]/Users/[short name of your account],it is a local account, authenticated by OD and not by /Local on this macintosh. In this case, the template to be use at user's first logging will be the /System/Library/User Template of this specific macintosh. If you really need any modification of the user's template, you should spread a new model prior to the first user's logging, either via deployment (modified system disk image) or via ARD, SSH or any other method.
But by far a better solution is to use MCX to modify your user's experience - and your's, by the way, because you'll be able to spread any policy in a snap, while modifying the user template is a one-shot. Are you really shure that MCX does'nt allow you to perform what you want ? Take a look to John de Troyes's litterature : here to download