It's ok to have the Road Hero facing down (without the bag) but that means you need to buffer the alloy wheel from touching the floor of the boot to avoid noise/vibration, rather than having the rubber tyre against the floor. I also think that the original Toyota alloy is not as concave as the Road Hero and may not present the same issue.
Agree about retaining bolt only necessary in extreme situations but the the fact is, there is always provision for one.