You're correct that the list of packages Blueprint deems important is
flattened as you describe. It keeps track of the dependent packages
so it can install the correct versions when applied later.
Blueprint isn't capable of removing packages, be they "top-level" or
dependencies, unfortunately, but if you `apt-get remove ...` or
`apt-get autoremove` and create a new blueprint you'll at least have a
record you can diff against.
I know that's not a complete solution to your problem but I hope it helps.
Richard