I have two questions regarding project bundles:
1) When using the Python API (export_bundle command) to create a project bundle, is there any way to specify which datasets should be included with the bundle? Specifically, I want to include any uploaded datasets.
2) When creating bundles to move to the Automation Node, is it possible to also include project permissions or is it necessary to re-create the project permissions when the project is imported to the Automation Node?
Indeed there's a way.
The bundle you create will do so using the project settings. Therefore, before you create it, modify the settings of the project. Depending on whether you use Python or HTTP rest API, the section to modify is
In order to get there, instantiate the project and modify the settings (obtain settings then edit the relevant part), see here for an example. Regarding the exact shape of what you need to enter, I find it easier to create through the UI and then inspect the resulting settings of the project in the API, that way I can modify programmatically later.
Regarding your second question, see for this post on a similar topic, after activating the project in Automation you can edit permissions and give access to the relevant groups.
FYI we just published a Knowledge Base article on this topic: How to add a group to a DSS Project using a Python Script.