The two center bolts do not go thru the cross member but bolt solidly to the front engine plate, they should use a lock nut and they should be tight.
There should be 1/16" +/_ 1/64" clearance between the lower steel retainer that holds the rubber mount and that upper cover plate you were asking about with the curved lip on the front side before the motor is bolted to the frame. The outer bolts do go thru the frame and should only be tightened down enough to maintain the clearance. Originally the bolts would have had castle nuts that were locked with cotter pins when the nut and bolt are snugged up. And alternative is to use Nylock nuts (elastic stop nut) and adjust them till it is snug, maintaining the 1/16" clearance.
You are instructed to file or grind the upper edge of the lower retainer if the clearance is less than 3/64". This is one of those odd-ball instructions because most people naturally want to torque the bolts that hold the motor to the frame down tight. It’s possible to close the gap up completely simply by tightening the nuts as you are instructed to do. In my opinion it should tell you to just snug the nuts up before locking the nut to the bolt. What I've done is to just make sure that the rubber is under some tension and that there is some clearance between the retainer and the cover plate.
You can read the instructions here if you care to:
http://chevy.oldcarmanualproject.com/shop/1954truck/54ctsm0613.htmlDenny Graham
Sandwich, IL