Regarding item 1.. this is typically part of a shelf deployment since they shelf resources. You could probably have a plugin install those preset resources into a shelf on init as long as you know what shelf they need to be put in. Deploying them with your project shelves is likely a better approach though for consistent asset interface and compatibility.
That said, I'm personally not a fan of the application template and export presets for large productions. They have little to no API visibility and must be manually maintained, which generally means they don't get maintained, and require a shelf re-deployment. If you have custom scene assemblers and exporters, your own JSON config might be an option to consider.
Regarding item 2.. Your plugins don't have to reside in the user docs directory. If you are controlling the user environment, you can add a custom plugins path via SUBSTANCE_PAINTER_PLUGINS_PATH. Keep in mind, the folder structure should match the expected user docs structure.