Is there a way I can specify box size for a graph builder plot? See highlighted image below. Box size does not include the axis label sizes. I want to make multiple plots with same box size. Frame size considers the size of the whole frame and not the box.

The Size(x,y) option will allow you to set the size of the whole plot and the number of subplots will automatically scale to fill in that space.
Graph Builder(
Size( x, y ),
Show Control Panel( 0 ),
Variables( X( :X ), Y( :Y ), Group X( :Group ) ),
Elements( Points( X, Y, Legend( 15 ) ), Smoother( X, Y, Legend( 16 ) ) )
);