I tend to keep some fuel in my tanks after every flying session as it helps to keep the in-tank tubing flexible, but every now and then I do empty them. The hole in the firewall thing in most cases is to aid in balancing the model by having the engine as far back as possible, but if that is not the case in your situation it's quite the norm to use standoffs. Painting the inside of the fuse ( fuel proofing) is commonplace and is protection against fuel spills like in the case of a broken line or tank.