Hi iblanco,
I'm running 3.3, but I'm looking to do the same thing. Have you found good documentation on creating new presets? I've been staring at presets.xml, slack-jawed and not sure what to do with it.
As for your proposed approaches… Your first approach makes the most sense to me and your second approach does smell like a dirty hack.
What do you think about creating a private site and making sure the required folders exist in there (ie, discussions, etc…), then applying a rule to folders created in the main Sites folder that executes a script? The script could copy the desired folders from your template site into the newly created site.
I'm just about to leave the office for the day, but I'll try this approach tomorrow and I'll post my results!