There are 3 general levels you can take with AMIs:
1) Vanilla instance AMI, have puppet/chef install everything for you, then fetch your app code and configure that
2) Use another tool to have your instance built with puppet/chef and then capture that into an AMI. Once it spins up it just needs to get your app code. Idea here is your services arent likely to need updated as fast as your app code.
3) Same as two, but when your production code is in release/maintenance mode, bake everything into an AMI. When you need to deploy new code, you need to create a new AMI, but you are creating an AMI with scripts so its no big deal :) All you have to do now is update your cloudformation
Obviously if you have a setup with rapidly deployed code changes you'll want to have your puppet manifest grab the latest version before deploying live when spinning up a new instance.
There's a reason many Vagrant boxes I see use Puppet to instantiate though: It's friggin simple to get started with. More advanced configurations might even end up requiring you to build your own modules and extended manifests, but I expect this configuration detailed in the article would probably amount to a couple hundred lines for the entire manifest.
I think this also underscores one of the things I like the most about Puppet (instead of Chef, which is a fine CM system as well); It's easy to get started with but powerful enough to get things done down the road. Honestly, there's never a better time to start working with Puppet than from the very beginning of a project!
If you wait until you've got a more complex configuration, you're fighting both the tool syntax and system setup requirements. Not to mention the clock that's ticking and telling you that you needed to be all up and running yesterday.
Essentially you pre-run a puppet manifest and have it do all the first-run processing and then store THAT as the AMI/instance. This way you have an instance that only needs a few seconds to get itself ready while also integrating configuration management (which really you should be doing these days). Just some suggestions from a sysadmin.