Hi Roland, welcome! Currently, there is not a way to manually arrange the platform list, unfortunately. If you'd like, you can add it and vote for it on our issues list here: https://bitbucket.org/jasondavidcarr/launchbox
Per #2, honestly I thought you could do that, but I looked and it appears you can't. It looks like we need more options there as well for specifying which images/videos show up underneath the box art.
For #3, I think people typically set up different platforms in that scenario, but what you could do if you want to keep the same platform, is add a second Retroarch emulator (not the files, just the emulator record in LaunchBox), and configure each differently and pick between the two when you're adding games for Sega CD.