I'd say Mega Flare is more reliable than Warpinator.
Mega Flare not only wipes out one wave or enemies; it wipes three. It does come with some drawback, though; it is fire-based so you can't damage enemies like Red Nocturnes and Wizards. Also, starting from Destiny Islands, I think it no longer one-shots Heartless, because it takes precisely one whole bar of HP while the enemies have one bar of HP plus a little bit.
On the contrary, Warpinator is non-elemental and can be used against all normal enemies. However, if I remember correctly, it could only remove enemies that are currently on-screen and the effect doesn't linger; meaning, it only wipes out one wave. In addition, as you said, it has a chance to miss, and enemies defeated with Warpinator don't give out EXP.
I suggest you go with Mega Flare, but compound it with another room-clearing sleights such as Tornado. If you're farming for White Mushroom cards, though, Warpinator is the best choice.
Oh, and the Key to Rewards can be gained at any time after the first Larxene battle. The odds increase with every floor you clear, and I think by Twilight Town, the chances of getting it at the first room of the world would have become comfortably likely.