I would want the output pdf to be stored in a storage account, specified upon request (assuming we have all the permissions sorted out).
The custom jsreport scripts hook afterRender is there to give you the option to upload the results somewhere.
https://jsreport.net/learn/scripts
The example in the documentation sends the output through email and you just need to change the script code to upload it as a blob to your storage.
I would like to get the input data for the same request from a specific blob location as well, the location of the file and storage account info will be provided in the request instead of the data.
Yes, this is the common flow as well. You can use beforeRender hook and actively download the input data from your services. It can be from blob, REST, database... There is no limitation and it is just up to you how you implement the hook body.