I was going to post yesterday that on the SBC/BBC the dots together means TDC for #6, but it doesn't really matter either way. When you rotate the crank two times then you have the cam gear dot at the top and you're at TDC #1, I am pretty sure the LS is the same. I just pulled my timing set off my 5.3 so I can't double check, but logically it seems the same. The crank doesn't do anything but move the pistons up and down, it's the cam that determines the valve timing.
The only other variable is the cam sensor, and then you would be 180 degrees out if the dots both need to be up
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