It is said in the wiki that 'Participants are required to develop parsimonious models (at most 100 total unique genes can be involved)'. It means 100 unique genes can be involved in one challenge or different task can use 100 unique genes.
Created by Fawne Challenge 2 has 2 prediction tasks: A and B. The maximum number of unique genes for challenge 2 is 100. For instance, in task A one can use 50 genes and in task B can use other 50 distinct genes. Another example is that for task A one uses 100 genes and for task B the participant uses 20 among the genes used in task A. So as long as the total unique genes is 100 or less, any scenario is compliant.