every guitar sounds a certain way, it has to do with the wood, the way it resonates, the pickups, everything on the guitar effects the sound slightly.
In that sense, 2 guitars of the the exact same make and model sound ever so slightly different. some sound a lot differnt.
Therefore, since everything effects the way the guitar resonates, to the very keen ear, there might be a slight difference in tone if you cut a portion of the wood away that is audible.
The jem doesn't sound 'different' with the grip because it always *had* one. If you were to fill the monkey grip with wood, it would probably change the tone a bit as well
Similarly, if you were to cut a chunk out of the other side of the jem, it would effect the tone too.
But I still say don't worry about it. But please, I highly reccomend getting it done professionally. It's a tough thing to do, and it'll look like poo poo if you don't know what your doing. Trust me.