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I was chasing kyogre/groudon in emerald, and their 1-hit KO's (even sheer cold) did not affect my rayquaza. Groudon's solarbeam had to charge, and they stayed asleep longer then normal. is this due to their so-called fear to the superior rayquaza, or is it something different?

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Let's see. Your Rayquaza is probably a higher level than Groudon and Kyogre, seeing as you trained it. OHKO moves always fail when used against a pokemon of a higher level than the user.

Groudon's Solarbeam had to charge up due to Rayquaza's special ability: Air Lock, which nullifies any and all weather effects, meaning the sun is no longer there to power Groudon's Solarbeam.

As for the sleeping, it can vary from time to time how long the pokemon is asleep. Pokemon can be asleep anywhere from one to seven turns, so you probably just got lucky.

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Yes, the explanation does cover every part of the question.
OHKO moves are calculated by your level minus your foe's level plus 30, so as long as the foe isn't 30 levels higher than you there is still a possibility of it working.
yes, but if the target is a higher level than user, it automatically fails regardless of any other factors.
I literally never thought I would find such a good explanation... I hope you one day answer all questions on the pokebase, and be the question master!
Notice how there is STILL only one answer. That is how good it is.