I actually use an entirely different Magnezone set on my rain team, which has proven to be destructive if the opponent has a Nattorei or a Forretress:
Magnezone @ Leftovers
Modest
EVs: 252 HP/252 SpA/4 Spe
-Substitute
-Charge Beam
-Thunder
-Hidden Power [Water]
You bring Magnezone into Nattorei while it sets up Rocks, set up a Substitute, and begin using Charge Beam to accumulate boosts. After Nattorei dies, you are often at +4 - +6 Special Attack, which practically guarantees a kill on the Pokemon that breaks your substitute.
Preferably, you should pair this with a Rapid Spinner, as Nattorei can easily set up 3 layers of spikes while you trap it with Magnezone. Two great rapid spinners on rain teams include Kabutops and Starmie, as they are both able to abuse the rain and have good offensive/defensive synergy with Magnezone.
Haha good times. This varient of Magnezone will actually fuck you up, since he guarantees a minimum of 1-2 KO's if he traps Nattorei / Forretress. Personally I dropped zone for Nattorei (I was tired of losing against sub DD Kingdra) but It was pretty good when I used it.