The first is that librem may need to make changes that cannot be accepted by upstream. It can be features they need to have now to keep users happy. But another example could be that they want their Riot to default to their homeserver and not to matrix.org. You don't want to wait until you get a trademark conflict with the main project.

The second reason could be that Librem has to market their brand. If they keep Riot for example, people type it in google and end up on the official riot site, then it may be hard for Librem to attract new users.