Why are stopovers exempt?

Stopovers are exempt because 144 hour visa free transit does not allow itineraries that have two mainland Chinese stops in a row. The reason for this is very simple. China, as practically every other country, performs immigration and customs procedures at the very first stop in China. So, when you land in Xiamen, although you consider it just as a stopover, you in reality enter the country because you will pass through immigration and customs control. In other words, your next flight to Chongqing is a purely domestic one as you have already entered the country. So, the conclusion is very simple, if you were not prevented from doing this, that would mean that you are allowed to travel within China almost as you wish and that is not the purpose and the nature of 144 hour visa free transit scheme. Its purpose and nature is to limit the international passengers traveling through China to enjoy up to 6 days visa free stay, but just within one transit area. I hope this explanation clarifies this aspect of 144 hour visa free transit scheme.