Right click on the legend entry that you don't want (Y1/X2) and select Transparency. Set the transparency to 0. Then do the same for Y2/X1. Then double-click the legend and uncheck the entries for Y1/X2 and Y2/X1.
Try running this code:
dt = New Table( "X1 Y1 X2 Y2", Add Rows( 5 ),
New Column( "x1", Numeric, Continuous, Format( "Best", 12 ),
Set Values( [1, 2, 3, 4, 5] )
),
New Column( "y1", Numeric, Continuous, Format( "Best", 12 ),
Set Values( [1, 2, 3, 1, 2] )
),
New Column( "x2", Numeric, Continuous, Format( "Best", 12 ),
Set Values( [2, 3, 4, 5, 6] )
),
New Column( "y2", Numeric, Continuous, Format( "Best", 12 ),
Set Values( [4, 5, 6, 4, 5] )
)
);
dt << Graph Builder(
Show Control Panel( 0 ),
Variables(
X( :x1 ),
X( :x2, Position( 1 ) ),
Y( :y1 ),
Y( :y2, Position( 1 ) )
),
Elements( Points( X( 1 ), X( 2 ), Y( 1 ), Y( 2 ), Legend( 7 ), Jitter( 1 ) ) ),
SendToReport( Dispatch( {}, "400", ScaleBox,
{Legend Model( 7,
Properties( 1, {Transparency( 0 )} ),
Properties( 2, {Transparency( 0 )} )
)}
),
Dispatch( {}, "400", LegendBox, {Position( {0, -1, -1, 1} )} )
)
);