doc: Clean up list of Fedora dependencies

Fixed several issues with the install instructions for Fedora:

- removed packages that are already pulled by "Development Tools" and "C
  Development Tools and Libraries" groups
- added missing "which" package needed for SDK installation script
- added python3-devel package (needed for some of the Python requirements)
  and install python3 instead of a fixed python38

Tested on a vanilla Fedora 39 Docker image.

Signed-off-by: Benjamin Cabé <benjamin@zephyrproject.org>