Question 1: Yes. Its overhead storage capabilty is limited, however, to flat items that don't weigh so much that they interfere with the driver. Securing these items is a must. Large area flat items, such as plywood, or anything with a small surface area that weighs under 10 pounds would probably be fine.
Question 2: Yes. The Jammock was designed for this, which is why it purposely does not cover the entire cab. The 4 inches of space at the front (between where the Jammock stops and the windshield begins) are there to enable you to operate the cams to secure/un-secure the OEM top. With an OEM top installed, you have a more secure load to execute the overhead storage. The straps are flat and do not interfere with the OEM top.
Awesome. This thing just gets better and better. Ha so is it possible to secure the rear side windows on top of it with the top down without them blowing away? Any suggestions?
I don't remember if he had any luck. If they are the soft windows, then I would say "absolutely", with the caveat that I would not drive anywhere without securing them. The Jammock recommendation of securing flat loads is to use a piece of rope or webbing, thread it through the footman loop and around the soundbar, on top of your load, and below the Jammock and tie it down.