No spark at all means you've got something else wrong.
Match the pulses on the diagram to the notches in the wheel and you will find that the alignment hole matches with the TDC #1 pulse which means that is the TDC #1 position on the wheel. So, that's where the sensor MUST be when the #1 piston is also at TDC.
The scope traces also confirm that's exactly how it works because the cam signal switches at the same time the crank sensor picks up the #1 TDC notch beside the alignment hole. The alignment hole and corresponding notch must be passing in front of the sensor at #1 TDC for the sensor to be capable of picking it up.
When you hold a LS1 crank so the alignment hole is to the right, the #1 crank throw is facing where it'd be at TDC.
The crank sensor goes into the block with the plug facing forwards.
Tons of people have done this before and got it to work without the need to pursue the question you are so concerned about.
Centering the sensor at the alignment hole is plenty close enough to get your engine running. If you need it to be exactly accurate then tune it with no spark advance and fine adjust the crank sensor to get the spark at exactly TDC. That's assuming your crank sensor bracket is very solid yet has some adjustment and you also have TDC marked on the balancer with a pointer that has been verified with a piston stop.
Assuming you have the sensor clearance minimized, I would try moving the sensor forwards or backwards a little with respect to the wheel.
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