When we use the term thermal gradient it simply means that the temperature is not exactly the same in all locations inside the unit. More importantly, there is a pattern to the heat distribution that makes a puppy comfortable, and better able to regulate its own body temperature.
We discovered how important the thermal gradient is when we developed what we thought would be better for the puppies. We developed an incubator that was considerably more uniform in floor surface temperature than the glass units. It took five months to develop and just 10 minutes to see that puppies hated it.
Puppies instinctively seek out the warmer and cooler parts of their environment. When their body temperature is too warm, they go to a cooler spot. If their body temperature is too cool they move to a warmer spot. This movement helps them be stronger sooner. If the temperature is too uniform they continue to look for a cooler spot and never really settle down.
The trick is to only give puppies good choices. This allows the fine tuning of body temperature to me more gradual and effective.