The wrap will not give you separate axes that can be changed. However, the By clause will, and if you put a Lineup Box() around the Graph Builder, you can get the results you want. Below is a sample script

Names Default To Here( 1 );
dt = Open( "$SAMPLE_DATA/semiconductor capability.jmp" );
nw = New Window( "Example",
Lineup Box( N Col( 3 ),
Graph Builder(
Size( 324, 293 ),
Show Control Panel( 0 ),
Variables( X( :NPN2 ), Y( :NPN1 ) ),
Elements( Points( X, Y, Legend( 1 ) ), Smoother( X, Y, Legend( 2 ) ) ),
by( :wafer )
)
)
);
Jim