I very rarely take a second spare on the roof rack. First spare is below the landcruiser, so no problems there. If second one is ever needed, which is unlikely: to take it off roll/throw off the roof rack. Grab a bottle of water and go looking for it in the scrub. Roll it back. To put the flat one away either put in the back of the vehicle or wait for a friend with a ute, two person lift from the ground into the tray, park vehicles next to each other, climb in the tray with friend and two person lift onto the roof rack. Yes it's not ideal but then again never had to do it in anger yet.
Ah and I would NOT do it with anything much larger than a landcruiser wheel!!!