I could be wrong, but I believe Factom is organized like that to make it possible for users of the system to not be affected by blockchain bloat. Instead of having to download the entire blockchain and filter it, Factom allows you to only download the data relevant to your application. I'm not sure Apostille/NEM has that same ability. Bloat may not be an issue now, but if either system had billions/trillions of entries, it could become an issue very fast.