A default loose, similar to the default-loose caused by Self-KO clause, also doesn't have its basis in game mechanics and is straying from cartridge play. To be simulating the games, it has to be purely on the honor system.
Not true. For purposes of ladder rating and tournament play, we can say "You lose if X" and define X to be anything we want. That's not changing the game itself, just what we consider victory. You can disqualify people for whatever reason you want. Putting multiple Pokemon to sleep (if playing under Wi-Fi rules) is another kind of sleep clause that we can enforce just fine. Obviously this would be a poor rule for freeze clause.
Going at this another route, despite precedence for its existence, Sleep Clause itself, no matter how its implemented, is technically altering game-mechanics of the cartridge games, which Smogon seeks to simulate.
Yes, Sleep Clause is currently implemented improperly. That doesn't mean we continue to implement future things improperly. I would favor a Wi-Fi vs. PBR system of determining game mechanics (where our current Sleep Clause is only possible with PBR mechanics, and all things that come with that).
Surely you don't mean to say the acid rain has even the slightest possibility of being intentional? Beyond the fact that it is completely nonsensical, unprecedented and undocumented, the fact that the damage is done (in the case of the four-weather glitch) by the Pokémon's own abilities, rather than the weather itself, smacks of mussed code.
The point isn't that this is necessarily what the developers intended, but rather, you can't tell whether any given thing is intentional or a bug. Maybe they meant to give Heracross X-Scissor. Maybe Chatter should be Sketchable. Perhaps they meant for Brick Break to not break screens when it hits a Ghost. That is all irrelevant. It doesn't matter what they meant to do, could have done, or should have done. All that matters is what they did.