Hey there.
I'm really not sure that there's anything I can do about the sound continuing into the title screen. Some other people have reported it as well, and the truth is, this plugin is only reusing the built in function that rpgmaker has to play videos. I suspect this is an issue in the engine itself, and I don't have the know-how to fix it.
The best suggestion I could think of was to have the final splash video just be a couple of frames of a black screen with no sound, so that if the skipping bug happens, there's no audio continuing.
I'm glad you solved the other problem on your own, I wouldn't have guessed that as the cause, although it makes sense. The two different video formats are for mobile and desktop deployment, so it should only keep one of the files on deployment depending on which platform you targeted. If both ended up in the folder, I could see how the engine could get confused.
~Ramza