Track 1 is, as you surmised, a dumb skit to inform you that THIS DISC WILL DESTROY YOUR CD PLAYER, DON'T PLAY IT. It's not used in the game, so we didn't bother translating it.
Track 2 is actually the message that plays when you try to run the game on the wrong System Card version (not 3.00), and is basically just an advertisement for the game. We did subtitle it, so if you're curious, try running the game on a version 2.1 or lower BIOS.
Tracks 10-14 seem to be brief "interviews" with the voice actresses for the five main characters. They don't play during the game either and are just bonuses for anyone listening to the audio tracks. I hear the issue you're talking about on track 13; as you say, this is on the Redump-verified dump, so it seems to be an editing or mastering error from the original disc.
Removing these tracks should work fine as long as you run the game correctly, though I can't absolutely guarantee it.
And if you really need to save space, you could probably cut tracks 17 and 18 down to about a minute or so. They decided to loop both of them for five full minutes, even though you'd never hear them for that long under any normal circumstances.