Basically, if the combination of the values of the three gems you are fusing is below one million, then the totem bonus is willing to adapt itself downward to facilitate making a semi. So, if your totem bonus is 4000 for example, and the gems you are fusing have value 333,000 each, then the sum of those values is 999,000 which is below one million. In this case, the 4000 bonus reduces to 999, so that the result is 999,999 as desired.
However, if the gems had 334,000 value each, then the sum is 1,002,000 which is over one million. In that case the ritual would result in a 1,006,000 gem (which is absolutely not what you want).
The same phenomenon occurs around value 2,999,997 when making perfect gems. If you put three 999,000 gems in your totem, the sum is 2,997,000 and the totem bonus would reduce to 2,997.
Edited by Aluce, 22 July 2017 - 10:22 AM.