Just wire the buttons separatly. It is easy to change the mame settings so that both buttons do the same thing.
Just configure player1 button 1 to be "x" or "y" (where "x" and "y" are the keys that you have assigned to the buttons)
I have configured my 2 player cabinet so that on single player game you can use either joystick/buttons. Left handed players just use the right joystick and the left buttons.
Seems like an awfull waste of inputs to me...it could be done that way...but I wouldn't. Then again, I wouldn't put buttons on both sides of the stick.
Pete, if you have to have both sets of buttons just go with your original idea and wire them to the same spot on the encoder (or from one button set to the other--same result)...and save those extra inputs.
It's just my opinion...but I'm right. 
Actually, in this case I disagree with Spaced Invader and agree with WPC MAME.
If you do like Spaced Invader says, then you will never be able to use the buttons for separate inputs, they will always activate the same key. In essence, you are loosing 6 buttons on your CP.
If you do as WPCMAME says, they will act the same in most games, but you will have the option to use them to do other functions in some games, if you wanted to.
This is assuming that you have enough inputs on the KeyWiz for each button to have a separate input.
Regarding the initial question, I am left handed, but arcade controls feel more natural to me with the joystick on the left and the buttons on the right, standard layout. OTOH, in Centipede, I always ended up crossing over my arms so I could control the t-ball with my left hand and fire with my right.
I also agree with Mahuti - I write and throw with my left hand, use scissors with my right hand (I think there weren't enough right-handed scissors when I was growing up). I move my mouse to the left side, but I don't like having the mouse buttons reversed b/c then it feels awkward if I need to do something on someone else's computer.