Photo by Jason Rogers.
To understand how this works, remember that microwaves heat food by bombarding it with microwave radiation. This creates an alternating electric field, which excites the water molecules in your food and forces them to spin as they try to line up with the field. As the water molecules spin, they dissipate energy in the form of heat. Other molecules in your food then absorb that heat, and before long the entire dish is piping hot.
In ovens where the magnetron isn't powerful or large enough to cover the inside of the cooking chamber, you can cook your food more evenly by putting the dish or container on the end of the carousel so it passes in and out of the path of the waveguide (where the microwaves are emitted and the field is the strongest.) The water molecules will spin more rapidly since both they and the field are in motion, and the result is hotter food.
It's worth noting that this trick works best in older microwave ovens, as newer ones use more efficient magnetrons that cover the cooking chamber more evenly. Even in the best case, you'll only get a marginal increase in power from one side of the cooking chamber to the other, but it could be enough to heat that Hot Pocket all the way through on the first try. Still, you're not going to cook a 5-minute TV dinner in 3 minutes with this trick; it's just more likely your food will be more evenly and thoroughly heated when the cooking time is up.