I mean the temperature inside the incubator, not the eggs.

Warm air rises. So the top of your incubator will have a different temp than the bottom if it is large enough. Much like how a rack system has variable temps between the levels as well.

If you only keep an eye on the temps in the middle, your eggs near the top can be at a higher temp because the air at the top gets warmer before the probe in the middle hits the desired temps. The boxes on the lower shelves would also be slower to incubate as they will be at a lower temp than the ones in the middle.

If your incubator has a fan to circulate the air, it will keep the temps from naturally settling and you'll have a more even temp through the entire setup.

This depends on the type of incubator you use. I'm using a homemade cooler version so with only one eggbox, I have no problems maintaining my desired temps in there. When you have an incubator with varying shelves, that can be much harder to maintain.