In case this is useful for anyone besides me, here is the correct way to thread the waist buckle onto a Scubapro X-Tek Pure Harness;
My sincere apologies for the Microsoft Paint drawing. The long end of the red line represents the end of the webbing that is attached to the rest of the harness, and the short end is the end that you have in your hand. The rest should be self-explanatory. Threading it this way results in the buckle pulling tight properly when buckled in, and also means the other end of the webbing can slide over the buckle properly when putting it on.
You don’t want to know how many times I put it on wrong before I figured this out. I swear that thing exists in n-dimensional space or something.