Why is 42 the seed used in RunPCA() in Seurat?
Given that it is virtually impossible for a human to predict what random numbers will be generated given a certain seed, and what effects they will have for a given application, the choice of the seed can be considered arbitrary.

What matters is that fixing the seed should fix the behaviour of the application. What seed has been chosen does not really matter, as long as it is documented.

The choice of 42 could therefore well come from one of the reasons you propose. Only the authors of the programs could confirm.