Could you put empty or nearly empty resource stocks at the top of the list? This would make it easier to identify which production needs increasing, especially with Pyanodon's large number of resources.
You can already do this in version 1.4.1: open Shift+G → Global Inventory and select “Quantity ascending”. You can also use “Fill ratio ascending” to sort by stock relative to each item's configured storage limit.
Could you add an option to automatically add each resource to storage with a quantity of X?
I'm not sure I understood correctly: do you mean adding a setting for the default storage limit of new items? For example, automatically setting their limit to 100 instead of 0, without having to configure every item individually?
Could all resources be made available through the logistic robot network, with the logic then handled from there?
You can already use Global Provider Chests to supply configured items from global storage to your logistic network. However, I don't see how to expose the entire global storage directly to the logistic network with the current API.