[AgentZero]

For point 1, you supply ship will still build up supplies even hiding in a storm. As for the second question, I think as long as there is cargo space somewhere, the newly constructed units will be placed in it. I remember building a similar ship to your refueler, except it had a SY on it as well. I used it to support a pair of carriers that were raiding enemy ships. Every time the carriers ran low on fighters, got damaged, or ran low on supplies, they nipped back to the fueling station for a top up.