The "Adjustment Block" assemblies allow you to adjust the pipes. It's doubtful that you'd be able to measure and drill the endplates accurately enough that the pipes will be level and parallel. If only it was that easy.
The holes on the four sides of the adjustment blocks are threaded for the bolts and the nuts are placed on the bolts before screwing them into the block. You turn the bolts in and out as needed to hold the pipe in the adjusted position, then turn the nut tight against the block to lock the bolt in position.
Hope this helps.