For most fills in graph builder, you can right click on the legend and select Transparency...
For example:
Open("$SAMPLE_DATA\Big Class.jmp");
Graph Builder(
Variables( X( :height ) ),
Elements( Histogram( X, Legend( 5 ) ) ),
SendToReport(
Dispatch(
{},
"400",
ScaleBox,
{Legend Model(
5,
Properties(
0,
{Fill Color( 5 ), Transparency( 0.5 )},
Item ID( "height", 1 )
)
)}
)
)
);