1) There is absolutely nothing wrong with a rare item spawning in a crate 1/1000 of the time.
2) If you would have taken the time to read the thread that you linked you would see that the plasma cannon is not the only way to get high scores. The 2nd ranked player on the leaderboard even says:
"Anyway, to get top 10 you have to basically get the jetpack, mattock or lots of bombs, and the key and chest (or sunglasses) by 1-2 (1-3 at least). Then you have to get nearly every gem into a diamond and continually get lucky with mattocks or bombs. "
3) Also you're complaining about high scores in a leaderboard for a random game. Someone is bound to get a better seed than you. That's why the daily challenge is there. So that everyone has an equal playing field.
1) Only if that rare item isn't insanely powerful...
2) I meant you observe that how most people state that you have to get the Plasma Cannon to get those high scores... as getting one lets you bomb an entire level. An Plasma Cannon is worth infinite bombs.
Besides, getting one Jetpack (and possibly, a Mattock) makes you somewhat rely on your skill too. Getting the Plasma Cannon requires you to complete the insanely hard Mothership... so why add items that's supposed to be bound to a challenge given freely.
The Plasma Cannon isn't the only way, but sure one of the way to achieve an insane high-score.
3) I agree, but the Plasma Cannon makes the difference extremely high. Plus, Spelunky is more based on skill, than on just plain luck.
Plus, there can be a crate that contains a Plasma Cannon, that some people will open it and some will not. It isn't there fault (is it?), but just plain bad luck (that could be solved). You may that it might also, happen with a shotgun or a jetpack, it the Plasma Cannon is much more powerful than that (in fact, maybe the most powerful weapon).
Nothing can break blocks better than the Plasma Cannon.