There are some controllers that switch between multiple zones and control each one independently every few seconds, but those aren't very common and considerable more expensive than conventional controllers.
Most people locate their probes in the middle of the rack, which is pretty sound advice. The only problem is that it really depends on your room temps. For example, the bottom rack in YOUR house might be 2 degrees cooler because your house is better insulated or has a basement whereas the bottom rack in MY house might be 8 degrees cooler because the floors are cold in my ramshackle former vacation cottage.
What does this mean in practice? If we both set our controller for 88 degrees at the middle rack, YOU'RE getting 86 while I'm only getting 80. 86 is likey fine, 80 is less than optimal.
Bottom line... IMO it really depends on your room. I feel its far better to err on the warm side rather than the cool side, so I would go closer to the bottom.