Personal side note: I’m not a fan of branding open source apps. It delays security updates and waters down the original brands; Riot and K9 have good reputations; Why not utilize those?
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.
This isn't valid. They could absolutely ship Riot with its existing branding, with a config set to use their (or any other) homeserver. The matrix.org homeserver just happens to be the default (at the moment).
If the user calls Librem support then they have figure out what is going on. Which costs money and they still have a frustrated user.
Branding is often not about what is technically or legally possible, but about creating the right perception with users.