No, it's not a bad rip. Many tracks in SotN have one XA track with the song's introduction and one playthrough of the main song, and a separate XA track for the second playthrough to avoid replaying the intro. See "Dracula Castle" for example.
That's true, but it's just a quick and dirty solution by Konami (SotN is tthe only game where we found this)... If you take a look at both "pieces" you'll notice that the Block-ID byte is in both files the same, in case of XA it means it is ONE track, not two or three or whatever.
BTW: There's still no loop info, even with 2 pieces of a song