Hi @Theo, and welcome to the forum!
Have you checked out the User Guide chapter for Blue Carbon? There is a section Identifying LULC Transitions with the Preprocessor that provides some idea of what the pre-processor does, although it might not be as detailed as you’d like (in which case, let me know and I’ll update it…) There is also sample data for the model, which you may have installed when you installed InVEST, which provides an example of the landcover maps, the table that is used to define them for the pre-processor, and also provides the output from the pre-processor, so you can see what the transition matrix looks like.
Under the hood, I think what the model is doing is overlaying the landcover rasters, and identifying pixels where the landcover changes between them. Based on this, it creates the matrix table, containing all of the landcover types, and an indication of where the landcover goes from blue carbon habitat to non-habitat (disturbance) remains blue carbon habitat (accumulation) or remains non-habitat (no carbon change).