The disk time was subtracted because it is in-memory system and when your compressed datasets fit into memory your disk subsystem hopefully will be irrelevant.
Look, disk time counts, whether it's hadoop loading it into the memory of a given machine, or you reading it from disk and transferring it into a GPU piece by piece.
Your "hopefully it will be irrelevant" is, well, crazy. I work for an employer with plenty of in-memory systems (very large ones in fact), and it certainly doesn't discount disk time. In fact, it matters a lot!