For the 1, no having a setting for default region would be overkill, the default region is set to Europe for neocd games because raine is made in Europe. I guess I could detect the current locale and use japan instead if the locale is japenese, but even that would be quite overkill. It's not a problem of correct or not, it's just the game is not recognized before the 1st part is loaded. Once it's loaded if you reset the name doesn't change, so it knows how to take the right settings. So if you really want to see this animation, there's just a rest for you.
It's not an emulation bug neither, the neocd console has a fixed region so it always plays all games using the same region. Here we choose to allow the player to set the region independently for each game. So that produces a difference, but my goal is once again not to emulate precisely the console itself, but just to support neocd games as well as we can, that's all. The games are good, but the console itself is not interesting.
For the 2, I'll try later without any configuration file although I doubt it will make any difference, but it's annoying, it's always longer to retrieve the files needed in this case.
I reproduce it very easily with last blade 2, but not samsho3, go figure... ! Anyway, it was probably here since the beginning of the sdl2 version, so quite some time ago already, but it's right we played less neocd games with that version, and it was the kind of thing which could happen. Anyway the fix is just 1 line, very easy to fix. It affects the games with a width of 320 (although for some reason it's not so obvious for me in samsho3, there might be some other parameters there).
Anyway it's fixed... thanks for the report !