Checking on my Hero Mode file that's in the middle of the first Eldin visit, Goro is indeed behind the Sacred Temple, but he doesn't know any details about the stones/walls yet; he just mentions that there are some things that respond to music. Which makes sense, since you aren't supposed to have the harp to activate them yet. He's also holding a map; I don't remember whether or not he still does that later.
I also decided to upgrade the Slingshot, then returned to Eldin; nothing unusual happened. It required Dusk Relics, which you indeed cannot get on a Normal Mode file before the first Eldin visit, but you should be able to get everything necessary for the upgrade by the end of the first Sacred Realm, which is long before the Bokoblin Base sequence.
Also, let's keep in mind that although it sounds like the file that uploaded the glitch was a Hero Mode file, the first file that reported the glitch was not. So other causes specific to Hero Mode don't sound likely.
If it is a Hero Mode file, it's even stranger that he didn't get the bottle in the Sealed Temple or the bird statues...
I was thinking that perhaps not activating the bird statues was some sort of self-imposed challenge, but some are activated, so that's kind of a bad theory.
I don't have the save that is the normal file, just a hero mode file. I'm going to start a normal file pretty soon and try everything I can think of. If it goes with the normal screw-up this game has, it's probably an NPC that you have to talk to that normal people wouldn't. If there's any NPC that might trigger it, my guess would be the fortune-teller. His house is particularly hard to find, and very few players would not only find it, but go there at night that early in the game. Since he does eventually get a sidequest (losing the crystal ball after being sent to learn the song by Levias), could it be possible that he could be the trigger for it? It's a longshot, but I suppose anything is. We haven't tested it yet, so if anyone has an early-game file and doesn't mind going through Skyview again, maybe try talking to him and then going to Eldin. We're going to go through it soon anyway, but if anyone has a save for that, it would be interesting to find out.
It'll be hard to reproduce what the guy did, especially because I've heard that it can happen after you start the pinwheel sequence for the windmills in Skyloft.
Which makes me remember another sequence break idea that people had--if one does skip the Gust Bellow/Leaf Blower/Dust Buster thing, then you won't be able to get into the thunderstorm, so we'll have to eventually get into the Lanayru Mine to get just it. I'm sure this has been mentioned, but I just remembered that.
Gonna be doing some testing stuff tonight, I'll report anything I find. If anything.
EDIT:
Sudden terrible thought. This is the only Zelda that has conversation trees. In other words, different responses to a choice you make. What if it's a specific combination of things that you have to choose? O.O That's horrifying.
