I am sorry I still don't under stand the flange statement. Mine has two oval holes in the middle that the bolts go through and no flange. Also it has an indent in the crossmember that looks like it should allow clearance for something. Not sure which side it is mounted on either. Here is a pic below.
You have a 2sp Power-glide transmission if you have that type of x member. Installs the same on the frame. It only goes one way as you will see the slope it has for the mounting. Don't sweat it. Put the engine & tranny in and then install x member. You will have it right if the bolts line up.