First of all, these branches are called "warp glitch" and "game end glitch", and they both address what's known as
Major skip glitch. It's the same thing as
Game-breaking glitch.
By definition, it's a
major skip setup/trick, because it cuts away most of the time of the fastest run without it. Another way to put it is that it improves a run by an
order of magnitude. And it's
NOT an intended setup/trick, therefore it's called a
glitch.
So judging by that, there's no way for a run with some sort of Major skip glitch to be slower than the fastest run without it. Because it sounds like a paradox and doesn't make sense to me. However, one can come up with a different type of a major skip glitch that would be faster than the known version of it. If the "game end glitch" run skips the the ending from level 3, and the newly found warp glitch skips from level 1 to the last boss, it'd likely be faster. There's also SRAM glitch, which can do anything, even what the above 2 glitches do, but it is only available if you corrupt SRAM. Finally, there are other types of major skip glitches, that can't be generalized by the 3 terms I mentioned, and we invent new names for them: "box glitch", "stairs glitch", "X-Ray glitch", etc.
Regarding Vault/Moons, it all depends on how entertaining the run is. Sometimes a branch that avoids the major skip glitch is published to Moons for being entertaining enough. Vault only accepts "fastest possible completion" and "full completion" goals, so if 2 glitched (as we used to call them all previously) runs are both very boring and deserve only Vault, we'll only publish one of them. But if they both deserve Moons, we will most likely obsolete one with the other, unless they are exceptionally different:
We've had
[1978] SNES Super Metroid "X-Ray glitch" by Cpadolf in 21:25.12 and
[2558] SNES Super Metroid "GT code, game end glitch" by amaurea, Cpadolf, total in 14:52.88
published alongside each other for a short while, and then they both got obsoleted by
[2600] SNES Super Metroid "game end glitch" by Cpadolf in 12:54.71.
