1. The key is chipped, so you will need to secure another key that is compatible for it. I'm surprised that Toyota dealership could not help you with this. I'd try another dealer or contact the BBB and see if this will "effect" a fix from your dealership. On my 2009 Matrix XRS - the remote and key were one unit - though that might have been a package deal.
2. Light should stop blinking once you use the key fob. But something sounds a bit off, the car shouldn't even be able to start without a chipped key - the light indicates that the key was accepted and the car can startup. I'd press on the dealership to see if they will work with you on the remotes.
3. No cargo net. Mine came with both the adjustable straps (to secure the full size tire in the event of a flat) and a collapsible fabric privacy deck hoop to cover the cargo area, but no net. D-rings are installed in the cargo area, but the netting was part of an option package.